diff --git a/DESCRIPTION b/DESCRIPTION
index f90032f19408d3931f539627e91c784c82266444..badf1f30e9ff77e3fd2b90ed65fd966ff7efb2cb 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: splatter
Type: Package
Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 1.5.0
-Date: 2018-05-02
+Version: 1.7.2
+Date: 2018-12-06
Author: Luke Zappia
Authors@R:
c(person("Luke", "Zappia", role = c("aut", "cre"),
@@ -60,10 +60,12 @@ Suggests:
phenopath,
BASiCS,
zinbwave,
- SparseDC
+ SparseDC,
+ BiocManager
biocViews: SingleCell, RNASeq, Transcriptomics, GeneExpression, Sequencing,
- Software
+ Software, ImmunoOncology
URL: https://github.com/Oshlack/splatter
BugReports: https://github.com/Oshlack/splatter/issues
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.1
+Encoding: UTF-8
VignetteBuilder: knitr
diff --git a/NEWS.md b/NEWS.md
index 9ac04f629bd292cfb67b38c64518a8abf991ce44..7d08f770935a5ddca6747a6efd1c58316b6199a6 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,8 +1,77 @@
-## Version 1.5.0 (2018-01-02)
+## Version 1.7.2 (2018-12-06)
+
+* Add ImmunoOncology biocViews tag at request of Bioconductor team
+
+## Version 1.7.1 (2018-11-17)
+
+* Fix bugs in vignette
+
+## Version 1.7.0 (2018-11-01)
+
+ * Bioconductor 3.9 devel
+
+## Version 1.6.1 (2018-12-06)
+
+* Add ImmunoOncology biocViews tag at request of Bioconductor team
+
+# Version 1.6.0 (2018-11-01)
+
+* Bioconductor 3.8 release
+
+## Version 1.5.8 (2018-10-22)
+
+* Add WithSpikes argument when calling BASiCS::BASiCS_MCMC()
+
+## Version 1.5.7 (2018-10-03)
+
+* Fix BASiCSEstimate tests
+
+## Version 1.5.4 (2018-08-30)
+
+* Fix installation instructions
+
+## Version 1.5.3 (2018-08-20)
+
+* Fix bug in BASiCSEstimate when no spike-ins provided
+
+### Version 1.5.2.9000 (2018-08-16)
+
+* Add missing regression argument to BASiCSEstimate
+* Add new BASiCS tests
+
+## Version 1.5.2 (2018-08-16)
+
+* Fix bug in getLNormFactors when reversing factors less than one
+* Update documentation to new Roxygen version (6.1.0)
+* Change varible name in vignette for compatibility with scater
+* Add suggested package checks to tests
+
+## Version 1.5.1 (2018-06-12)
+
+* Fix normality testing error in splatEstLib
+* Correct p-value cutoff in normality test
+* Sample library sizes for normality testing if > 5000 cells
+
+## Version 1.5.0 (2018-05-02)
* Bioconductor 3.7 devel
-# Version 1.4.0 (2018-01-02)
+## Version 1.4.3 (2018-08-20)
+
+* Fix bug in BASiCSEstimate when no spike-ins provided
+
+## Version 1.4.2 (2018-08-16)
+
+* Add missing regression argument to BASiCSEstimate
+* Add new BASiCS tests
+
+## Version 1.4.1 (2018-06-12)
+
+* Fix normality testing error in splatEstLib
+* Correct p-value cutoff in normality test
+* Sample library sizes for normality testing if > 5000 cells
+
+# Version 1.4.0 (2018-05-02)
* Bioconductor 3.7 release
diff --git a/R/BASiCS-estimate.R b/R/BASiCS-estimate.R
index cfbea4606a91ae41e95c2363fa74de71766d2025..f3148eda55932c2113611772f2a272329bfc5449 100644
--- a/R/BASiCS-estimate.R
+++ b/R/BASiCS-estimate.R
@@ -14,6 +14,8 @@
#' @param thin thining period for the MCMC sampler. Must be \code{>= 2}.
#' @param burn burn-in period for the MCMC sampler. Must be in the range
#' \code{1 <= burn < n} and a multiple of \code{thin}.
+#' @param regression logical. Whether to use regression to identify
+#' over-dispersion. See \code{\link[BASiCS]{BASiCS_MCMC}} for details.
#' @param params BASiCSParams object to store estimated values in.
#' @param verbose logical. Whether to print progress messages.
#' @param progress logical. Whether to print additional BASiCS progress
@@ -38,13 +40,14 @@
#' spike.info <- data.frame(Name = rownames(sc_example_counts)[1:10],
#' Input = rnorm(10, 500, 200),
#' stringsAsFactors = FALSE)
-#' params <- BASiCSEstimate(sc_example_counts[1:50, 1:20],
+#' params <- BASiCSEstimate(sc_example_counts[1:100, 1:30],
#' spike.info)
#' params
#' }
#' @export
BASiCSEstimate <- function(counts, spike.info = NULL, batch = NULL,
n = 20000, thin = 10, burn = 5000,
+ regression = TRUE,
params = newBASiCSParams(), verbose = TRUE,
progress = TRUE, ...) {
UseMethod("BASiCSEstimate")
@@ -55,6 +58,7 @@ BASiCSEstimate <- function(counts, spike.info = NULL, batch = NULL,
BASiCSEstimate.SingleCellExperiment <- function(counts, spike.info = NULL,
batch = NULL, n = 20000,
thin = 10, burn = 5000,
+ regression = TRUE,
params = newBASiCSParams(),
verbose = TRUE, progress = TRUE,
...) {
@@ -66,6 +70,7 @@ BASiCSEstimate.SingleCellExperiment <- function(counts, spike.info = NULL,
#' @export
BASiCSEstimate.matrix <- function(counts, spike.info = NULL, batch = NULL,
n = 20000, thin = 10, burn = 5000,
+ regression = TRUE,
params = newBASiCSParams(), verbose = TRUE,
progress = TRUE, ...) {
@@ -107,21 +112,28 @@ BASiCSEstimate.matrix <- function(counts, spike.info = NULL, batch = NULL,
if ((burn %% thin) != 0) {
stop("'burn' must be a multiple of 'thin'")
}
+ checkmate::assertFlag(regression)
is.spike <- rownames(counts) %in% spike.info$Name
+
BASiCS.data <- suppressMessages(
BASiCS::newBASiCS_Data(counts, is.spike, spike.info,
batch)
)
+ with.spikes <- sum(is.spike) > 1
+
if (verbose) {
mcmc <- BASiCS::BASiCS_MCMC(Data = BASiCS.data, N = n, Thin = thin,
- Burn = burn, PrintProgress = progress, ...)
+ Burn = burn, Regression = regression,
+ PrintProgress = progress,
+ WithSpikes = with.spikes, ...)
} else {
mcmc <- suppressMessages(
BASiCS::BASiCS_MCMC(Data = BASiCS.data, N = n, Thin = thin,
- Burn = burn, PrintProgress = progress,
- ...)
+ Burn = burn, Regression = regression,
+ PrintProgress = progress,
+ WithSpikes = with.spikes, ...)
)
}
@@ -129,7 +141,11 @@ BASiCSEstimate.matrix <- function(counts, spike.info = NULL, batch = NULL,
means <- BASiCS::displaySummaryBASiCS(mcmc.summ, Param = "mu")[, 1]
deltas <- BASiCS::displaySummaryBASiCS(mcmc.summ, Param = "delta")[, 1]
- phis <- BASiCS::displaySummaryBASiCS(mcmc.summ, Param = "phi")[, 1]
+ if (!is.null(spike.info)) {
+ phis <- BASiCS::displaySummaryBASiCS(mcmc.summ, Param = "phi")[, 1]
+ } else {
+ phis <- rep(1, ncol(counts))
+ }
ss <- BASiCS::displaySummaryBASiCS(mcmc.summ, Param = "s")[, 1]
thetas <- BASiCS::displaySummaryBASiCS(mcmc.summ, Param = "theta")[, 1]
diff --git a/R/splat-estimate.R b/R/splat-estimate.R
index 5af464671d321fa45e8ef299285995b155cc2b78..0af1ceda491b3fecd84b28a77dbc5fe15a539eed 100644
--- a/R/splat-estimate.R
+++ b/R/splat-estimate.R
@@ -101,7 +101,7 @@ splatEstMean <- function(norm.counts, params) {
#' Estimate Splat library size parameters
#'
-#' The Shapiro-Wilk test is used to determine if the library sizes are
+#' The Shapiro-Wilks test is used to determine if the library sizes are
#' normally distributed. If so a normal distribution is fitted to the library
#' sizes, if not (most cases) a log-normal distribution is fitted and the
#' estimated parameters are added to the params object. See
@@ -116,8 +116,17 @@ splatEstMean <- function(norm.counts, params) {
splatEstLib <- function(counts, params) {
lib.sizes <- colSums(counts)
- norm.test <- shapiro.test(lib.sizes)
- lib.norm <- norm.test$p.value < 0.05
+
+ if (length(lib.sizes) > 5000) {
+ message("NOTE: More than 5000 cells provided. ",
+ "5000 sampled library sizes will be used to test normality.")
+ lib.sizes.sampled <- sample(lib.sizes, 5000, replace = FALSE)
+ } else {
+ lib.sizes.sampled <- lib.sizes
+ }
+
+ norm.test <- shapiro.test(lib.sizes.sampled)
+ lib.norm <- norm.test$p.value > 0.2
if (lib.norm) {
fit <- fitdistrplus::fitdist(lib.sizes, "norm")
diff --git a/R/splat-simulate.R b/R/splat-simulate.R
index 5b94b1e8a21138f7c8c4209ab2ccda79fc33f4aa..fbf9ff108ee00818bad3dd531425f9c704bb8568 100644
--- a/R/splat-simulate.R
+++ b/R/splat-simulate.R
@@ -212,7 +212,7 @@ splatSimulate <- function(params = newSplatParams(),
}
if (verbose) {message("Simulating BCV...")}
sim <- splatSimBCVMeans(sim, params)
- if (verbose) {message("Simulating counts..")}
+ if (verbose) {message("Simulating counts...")}
sim <- splatSimTrueCounts(sim, params)
if (verbose) {message("Simulating dropout (if needed)...")}
sim <- splatSimDropout(sim, params)
@@ -819,8 +819,7 @@ getLNormFactors <- function(n.facs, sel.prob, neg.prob, fac.loc, fac.scale) {
dir.selected <- (-1) ^ rbinom(n.selected, 1, neg.prob)
facs.selected <- rlnorm(n.selected, fac.loc, fac.scale)
# Reverse directions for factors that are less than one
- dir.selected[facs.selected < 1 & dir.selected == -1] <- 1
- dir.selected[facs.selected < 1 & dir.selected == 1] <- -1
+ dir.selected[facs.selected < 1] <- -1 * dir.selected[facs.selected < 1]
factors <- rep(1, n.facs)
factors[is.selected] <- facs.selected ^ dir.selected
diff --git a/README.md b/README.md
index b53a44dbe29bb8b3596a7019fc7277eec8ae0023..7b85bef86d225e7da1c40529f05fc5cbb8334bbc 100644
--- a/README.md
+++ b/README.md
@@ -26,18 +26,18 @@ simulations and real datasets.
Splatter is available from [Bioconductor][bioc] for R >=3.4.
-If you have this installed Splatter can be installed from Bioconductor using
-`biocLite`:
+It can be installed from Bioconductor with:
```{r}
-source("https://bioconductor.org/biocLite.R")
-biocLite("splatter")
+if (!requireNamespace("BiocManager", quietly=TRUE))
+ install.packages("BiocManager")
+BiocManager::install("splatter")
```
If you wish to build a local version of the vignette use:
```{r}
-biocLite("splatter", build_vignettes=TRUE)
+BiocManager::install("splatter", build_vignettes=TRUE)
```
This will also build the vignette and install all suggested dependencies (which
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
new file mode 100644
index 0000000000000000000000000000000000000000..8bd38ffb016a9718c3ca5ce21ad107b9fa9d4717
--- /dev/null
+++ b/docs/LICENSE-text.html
@@ -0,0 +1,815 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
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+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
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+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
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+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
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+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="pkgdown.css" rel="stylesheet">
+<script src="pkgdown.js"></script>
+
+
+
+ <link href="extra.css" rel="stylesheet">
+
+<meta property="og:title" content="License" />
+
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
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+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
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+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+
+ gtag('config', 'UA-52309538-4');
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+ </head>
+
+ <body>
+ <div class="container template-title-body">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
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+ <a href="articles/splatter.html">Get started</a>
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+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
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+
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+</div><!--/.navbar -->
+
+
+ </header>
+
+<div class="row">
+ <div class="contents col-md-9">
+ <div class="page-header">
+ <h1>License</h1>
+ </div>
+
+<pre> GNU GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
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+ "Additional permissions" are terms that supplement the terms of this
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+Additional permissions that are applicable to the entire Program shall
+be treated as though they were included in this License, to the extent
+that they are valid under applicable law. If additional permissions
+apply only to part of the Program, that part may be used separately
+under those permissions, but the entire Program remains governed by
+this License without regard to the additional permissions.
+
+ When you convey a copy of a covered work, you may at your option
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+ 8. Termination.
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+ You may not propagate or modify a covered work except as expressly
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+ Termination of your rights under this section does not terminate the
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+ 9. Acceptance Not Required for Having Copies.
+
+ You are not required to accept this License in order to receive or
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+
+ 10. Automatic Licensing of Downstream Recipients.
+
+ Each time you convey a covered work, the recipient automatically
+receives a license from the original licensors, to run, modify and
+propagate that work, subject to this License. You are not responsible
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+
+ An "entity transaction" is a transaction transferring control of an
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+not impose a license fee, royalty, or other charge for exercise of
+rights granted under this License, and you may not initiate litigation
+(including a cross-claim or counterclaim in a lawsuit) alleging that
+any patent claim is infringed by making, using, selling, offering for
+sale, or importing the Program or any portion of it.
+
+ 11. Patents.
+
+ A "contributor" is a copyright holder who authorizes use under this
+License of the Program or a work on which the Program is based. The
+work thus licensed is called the contributor's "contributor version".
+
+ A contributor's "essential patent claims" are all patent claims
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+hereafter acquired, that would be infringed by some manner, permitted
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+(such as an express permission to practice a patent or covenant not to
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+available, or (2) arrange to deprive yourself of the benefit of the
+patent license for this particular work, or (3) arrange, in a manner
+consistent with the requirements of this License, to extend the patent
+license to downstream recipients. "Knowingly relying" means you have
+actual knowledge that, but for the patent license, your conveying the
+covered work in a country, or your recipient's use of the covered work
+in a country, would infringe one or more identifiable patents in that
+country that you have reason to believe are valid.
+
+ If, pursuant to or in connection with a single transaction or
+arrangement, you convey, or propagate by procuring conveyance of, a
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+receiving the covered work authorizing them to use, propagate, modify
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+you grant is automatically extended to all recipients of the covered
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+
+ A patent license is "discriminatory" if it does not include within
+the scope of its coverage, prohibits the exercise of, or is
+conditioned on the non-exercise of one or more of the rights that are
+specifically granted under this License. You may not convey a covered
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+in the business of distributing software, under which you make payment
+to the third party based on the extent of your activity of conveying
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+or that patent license was granted, prior to 28 March 2007.
+
+ Nothing in this License shall be construed as excluding or limiting
+any implied license or other defenses to infringement that may
+otherwise be available to you under applicable patent law.
+
+ 12. No Surrender of Others' Freedom.
+
+ If conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License. If you cannot convey a
+covered work so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you may
+not convey it at all. For example, if you agree to terms that obligate you
+to collect a royalty for further conveying from those to whom you convey
+the Program, the only way you could satisfy both those terms and this
+License would be to refrain entirely from conveying the Program.
+
+ 13. Use with the GNU Affero General Public License.
+
+ Notwithstanding any other provision of this License, you have
+permission to link or combine any covered work with a work licensed
+under version 3 of the GNU Affero General Public License into a single
+combined work, and to convey the resulting work. The terms of this
+License will continue to apply to the part which is the covered work,
+but the special requirements of the GNU Affero General Public License,
+section 13, concerning interaction through a network will apply to the
+combination as such.
+
+ 14. Revised Versions of this License.
+
+ The Free Software Foundation may publish revised and/or new versions of
+the GNU General Public License from time to time. Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+ Each version is given a distinguishing version number. If the
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+version or of any later version published by the Free Software
+Foundation. If the Program does not specify a version number of the
+GNU General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+ If the Program specifies that a proxy can decide which future
+versions of the GNU General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+ Later license versions may give you additional or different
+permissions. However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+ 15. Disclaimer of Warranty.
+
+ THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+ 16. Limitation of Liability.
+
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ {one line to give the program's name and a brief idea of what it does.}
+ Copyright (C) {year} {name of author}
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+ If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+ {project} Copyright (C) {year} {fullname}
+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+ The GNU General Public License does not permit incorporating your program
+into proprietary programs. If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library. If this is what you want to do, use the GNU Lesser General
+Public License instead of this License. But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.
+</pre>
+
+ </div>
+
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+ </body>
+</html>
+
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 1adddb0175656c9edce00230fb7379a0b1600a0f..043ae7079c1c83274d04e2359a79afb0cb37e0cc 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -18,13 +18,24 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Articles" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,22 +45,20 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
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- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
<body>
- <div class="container template-vignette-index">
+ <div class="container template-article-index">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
@@ -59,8 +68,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +83,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +101,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,12 +109,12 @@
</header>
- <div class="page-header">
- <h1>Articles <small>version 1.5.0</small></h1>
-</div>
-
<div class="row">
- <div class="col-md-9">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Articles</h1>
+ </div>
+
<div class="section ">
<h3>All vignettes</h3>
<p class="section-desc"></p>
@@ -124,5 +138,8 @@
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/articles/splatter.html b/docs/articles/splatter.html
index 92425d11a47c49fd5d6739e30bded4e453bdd38d..a4b3f324eac313f90a96afff2f366e377afd4b9b 100644
--- a/docs/articles/splatter.html
+++ b/docs/articles/splatter.html
@@ -8,24 +8,24 @@
<title>Introduction to Splatter • Splatter</title>
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+ <div class="container template-article">
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@@ -34,8 +34,12 @@
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- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
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+
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@@ -45,13 +49,13 @@
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- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
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<a href="../reference/index.html">Reference</a>
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- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
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@@ -71,17 +75,20 @@
</header><div class="row">
- <div class="col-md-9">
+ <div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1>Introduction to Splatter</h1>
<h4 class="author">Luke Zappia</h4>
- <h4 class="date">2018-05-02</h4>
- </div>
+ <h4 class="date">2018-11-02</h4>
+
+ <small class="dont-index">Source: <a href="https://github.com/Oshlack/splatter/blob/master/vignettes/splatter.Rmd"><code>vignettes/splatter.Rmd</code></a></small>
+ <div class="hidden name"><code>splatter.Rmd</code></div>
+
+ </div>
-<div class="contents">
<div class="figure">
<img src="splatter-logo-small.png" alt="Splatter logo"><p class="caption">Splatter logo</p>
</div>
@@ -90,10 +97,11 @@
<h1 class="hasAnchor">
<a href="#installation" class="anchor"></a>Installation</h1>
<p>Splatter can be installed from Bioconductor:</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw">source</span>(<span class="st">"https://bioconductor.org/biocLite.R"</span>)</a>
-<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="kw">biocLite</span>(<span class="st">"splatter"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="cf">if</span> (<span class="op">!</span><span class="kw">requireNamespace</span>(<span class="st">"BiocManager"</span>, <span class="dt">quietly=</span><span class="ot">TRUE</span>))</a>
+<a class="sourceLine" id="cb1-2" data-line-number="2"> <span class="kw">install.packages</span>(<span class="st">"BiocManager"</span>)</a>
+<a class="sourceLine" id="cb1-3" data-line-number="3">BiocManager<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/BiocManager/topics/install">install</a></span>(<span class="st">"splatter"</span>)</a></code></pre></div>
<p>To install the most recent development version from Github use:</p>
-<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1"><span class="kw">biocLite</span>(<span class="st">"Oshlack/splatter"</span>, <span class="dt">dependencies =</span> <span class="ot">TRUE</span>,</a>
+<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">BiocManager<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/BiocManager/topics/install">install</a></span>(<span class="st">"Oshlack/splatter"</span>, <span class="dt">dependencies =</span> <span class="ot">TRUE</span>,</a>
<a class="sourceLine" id="cb2-2" data-line-number="2"> <span class="dt">build_vignettes =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
</div>
<div id="quickstart" class="section level1">
@@ -171,10 +179,9 @@
## filter</code></pre>
<div class="sourceCode" id="cb34"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb34-1" data-line-number="1"><span class="kw">data</span>(<span class="st">"sc_example_counts"</span>)</a>
<a class="sourceLine" id="cb34-2" data-line-number="2"><span class="co"># Estimate parameters from example data</span></a>
-<a class="sourceLine" id="cb34-3" data-line-number="3">params <-<span class="st"> </span><span class="kw"><a href="../reference/splatEstimate.html">splatEstimate</a></span>(sc_example_counts)</a></code></pre></div>
-<pre><code>## NOTE: Library sizes have been found to be normally distributed instead of log-normal. You may want to check this is correct.</code></pre>
-<div class="sourceCode" id="cb36"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb36-1" data-line-number="1"><span class="co"># Simulate data using estimated parameters</span></a>
-<a class="sourceLine" id="cb36-2" data-line-number="2">sim <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(params)</a></code></pre></div>
+<a class="sourceLine" id="cb34-3" data-line-number="3">params <-<span class="st"> </span><span class="kw"><a href="../reference/splatEstimate.html">splatEstimate</a></span>(sc_example_counts)</a>
+<a class="sourceLine" id="cb34-4" data-line-number="4"><span class="co"># Simulate data using estimated parameters</span></a>
+<a class="sourceLine" id="cb34-5" data-line-number="5">sim <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(params)</a></code></pre></div>
<pre><code>## Getting parameters...</code></pre>
<pre><code>## Creating simulation object...</code></pre>
<pre><code>## Simulating library sizes...</code></pre>
@@ -315,14 +322,14 @@
<h1 class="hasAnchor">
<a href="#the-splatparams-object" class="anchor"></a>The <code>SplatParams</code> object</h1>
<p>All the parameters for the Splat simulation are stored in a <code>SplatParams</code> object. Let’s create a new one and see what it looks like.</p>
-<div class="sourceCode" id="cb45"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb45-1" data-line-number="1">params <-<span class="st"> </span><span class="kw"><a href="../reference/newParams.html">newSplatParams</a></span>()</a>
-<a class="sourceLine" id="cb45-2" data-line-number="2">params</a></code></pre></div>
+<div class="sourceCode" id="cb43"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb43-1" data-line-number="1">params <-<span class="st"> </span><span class="kw"><a href="../reference/newParams.html">newSplatParams</a></span>()</a>
+<a class="sourceLine" id="cb43-2" data-line-number="2">params</a></code></pre></div>
<pre><code>## A Params object of class SplatParams
## Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'
##
## Global:
## (Genes) (Cells) [Seed]
-## 10000 100 498429
+## 10000 100 477689
##
## 28 additional parameters
##
@@ -368,17 +375,17 @@
<h2 class="hasAnchor">
<a href="#getting-and-setting" class="anchor"></a>Getting and setting</h2>
<p>If we want to look at a particular parameter, for example the number of genes to simulate, we can extract it using the <code>getParam</code> function:</p>
-<div class="sourceCode" id="cb47"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb47-1" data-line-number="1"><span class="kw"><a href="../reference/getParam.html">getParam</a></span>(params, <span class="st">"nGenes"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb45"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb45-1" data-line-number="1"><span class="kw"><a href="../reference/getParam.html">getParam</a></span>(params, <span class="st">"nGenes"</span>)</a></code></pre></div>
<pre><code>## [1] 10000</code></pre>
<p>Alternatively, to give a parameter a new value we can use the <code>setParam</code> function:</p>
-<div class="sourceCode" id="cb49"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb49-1" data-line-number="1">params <-<span class="st"> </span><span class="kw"><a href="../reference/setParam.html">setParam</a></span>(params, <span class="st">"nGenes"</span>, <span class="dv">5000</span>)</a>
-<a class="sourceLine" id="cb49-2" data-line-number="2"><span class="kw"><a href="../reference/getParam.html">getParam</a></span>(params, <span class="st">"nGenes"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb47"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb47-1" data-line-number="1">params <-<span class="st"> </span><span class="kw"><a href="../reference/setParam.html">setParam</a></span>(params, <span class="st">"nGenes"</span>, <span class="dv">5000</span>)</a>
+<a class="sourceLine" id="cb47-2" data-line-number="2"><span class="kw"><a href="../reference/getParam.html">getParam</a></span>(params, <span class="st">"nGenes"</span>)</a></code></pre></div>
<pre><code>## [1] 5000</code></pre>
<p>If we want to extract multiple parameters (as a list) or set multiple parameters we can use the <code>getParams</code> or <code>setParams</code> functions:</p>
-<div class="sourceCode" id="cb51"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb51-1" data-line-number="1"><span class="co"># Set multiple parameters at once (using a list)</span></a>
-<a class="sourceLine" id="cb51-2" data-line-number="2">params <-<span class="st"> </span><span class="kw"><a href="../reference/setParams.html">setParams</a></span>(params, <span class="dt">update =</span> <span class="kw">list</span>(<span class="dt">nGenes =</span> <span class="dv">8000</span>, <span class="dt">mean.rate =</span> <span class="fl">0.5</span>))</a>
-<a class="sourceLine" id="cb51-3" data-line-number="3"><span class="co"># Extract multiple parameters as a list</span></a>
-<a class="sourceLine" id="cb51-4" data-line-number="4"><span class="kw"><a href="../reference/getParams.html">getParams</a></span>(params, <span class="kw">c</span>(<span class="st">"nGenes"</span>, <span class="st">"mean.rate"</span>, <span class="st">"mean.shape"</span>))</a></code></pre></div>
+<div class="sourceCode" id="cb49"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb49-1" data-line-number="1"><span class="co"># Set multiple parameters at once (using a list)</span></a>
+<a class="sourceLine" id="cb49-2" data-line-number="2">params <-<span class="st"> </span><span class="kw"><a href="../reference/setParams.html">setParams</a></span>(params, <span class="dt">update =</span> <span class="kw">list</span>(<span class="dt">nGenes =</span> <span class="dv">8000</span>, <span class="dt">mean.rate =</span> <span class="fl">0.5</span>))</a>
+<a class="sourceLine" id="cb49-3" data-line-number="3"><span class="co"># Extract multiple parameters as a list</span></a>
+<a class="sourceLine" id="cb49-4" data-line-number="4"><span class="kw"><a href="../reference/getParams.html">getParams</a></span>(params, <span class="kw">c</span>(<span class="st">"nGenes"</span>, <span class="st">"mean.rate"</span>, <span class="st">"mean.shape"</span>))</a></code></pre></div>
<pre><code>## $nGenes
## [1] 8000
##
@@ -387,15 +394,15 @@
##
## $mean.shape
## [1] 0.6</code></pre>
-<div class="sourceCode" id="cb53"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb53-1" data-line-number="1"><span class="co"># Set multiple parameters at once (using additional arguments)</span></a>
-<a class="sourceLine" id="cb53-2" data-line-number="2">params <-<span class="st"> </span><span class="kw"><a href="../reference/setParams.html">setParams</a></span>(params, <span class="dt">mean.shape =</span> <span class="fl">0.5</span>, <span class="dt">de.prob =</span> <span class="fl">0.2</span>)</a>
-<a class="sourceLine" id="cb53-3" data-line-number="3">params</a></code></pre></div>
+<div class="sourceCode" id="cb51"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb51-1" data-line-number="1"><span class="co"># Set multiple parameters at once (using additional arguments)</span></a>
+<a class="sourceLine" id="cb51-2" data-line-number="2">params <-<span class="st"> </span><span class="kw"><a href="../reference/setParams.html">setParams</a></span>(params, <span class="dt">mean.shape =</span> <span class="fl">0.5</span>, <span class="dt">de.prob =</span> <span class="fl">0.2</span>)</a>
+<a class="sourceLine" id="cb51-3" data-line-number="3">params</a></code></pre></div>
<pre><code>## A Params object of class SplatParams
## Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'
##
## Global:
## (GENES) (Cells) [Seed]
-## 8000 100 498429
+## 8000 100 477689
##
## 28 additional parameters
##
@@ -438,8 +445,8 @@
## 0.8</code></pre>
<p>The parameters with have changed are now shown in ALL CAPS to indicate that they been changed form the default.</p>
<p>We can also set parameters directly when we call <code>newSplatParams</code>:</p>
-<div class="sourceCode" id="cb55"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb55-1" data-line-number="1">params <-<span class="st"> </span><span class="kw"><a href="../reference/newParams.html">newSplatParams</a></span>(<span class="dt">lib.loc =</span> <span class="dv">12</span>, <span class="dt">lib.scale =</span> <span class="fl">0.6</span>)</a>
-<a class="sourceLine" id="cb55-2" data-line-number="2"><span class="kw"><a href="../reference/getParams.html">getParams</a></span>(params, <span class="kw">c</span>(<span class="st">"lib.loc"</span>, <span class="st">"lib.scale"</span>))</a></code></pre></div>
+<div class="sourceCode" id="cb53"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb53-1" data-line-number="1">params <-<span class="st"> </span><span class="kw"><a href="../reference/newParams.html">newSplatParams</a></span>(<span class="dt">lib.loc =</span> <span class="dv">12</span>, <span class="dt">lib.scale =</span> <span class="fl">0.6</span>)</a>
+<a class="sourceLine" id="cb53-2" data-line-number="2"><span class="kw"><a href="../reference/getParams.html">getParams</a></span>(params, <span class="kw">c</span>(<span class="st">"lib.loc"</span>, <span class="st">"lib.scale"</span>))</a></code></pre></div>
<pre><code>## $lib.loc
## [1] 12
##
@@ -451,24 +458,23 @@
<h1 class="hasAnchor">
<a href="#estimating-parameters" class="anchor"></a>Estimating parameters</h1>
<p>Splat allows you to estimate many of it’s parameters from a data set containing counts using the <code>splatEstimate</code> function.</p>
-<div class="sourceCode" id="cb57"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb57-1" data-line-number="1"><span class="co"># Check that sc_example counts is an integer matrix</span></a>
-<a class="sourceLine" id="cb57-2" data-line-number="2"><span class="kw">class</span>(sc_example_counts)</a></code></pre></div>
+<div class="sourceCode" id="cb55"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb55-1" data-line-number="1"><span class="co"># Check that sc_example counts is an integer matrix</span></a>
+<a class="sourceLine" id="cb55-2" data-line-number="2"><span class="kw">class</span>(sc_example_counts)</a></code></pre></div>
<pre><code>## [1] "matrix"</code></pre>
-<div class="sourceCode" id="cb59"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb59-1" data-line-number="1"><span class="kw">typeof</span>(sc_example_counts)</a></code></pre></div>
+<div class="sourceCode" id="cb57"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb57-1" data-line-number="1"><span class="kw">typeof</span>(sc_example_counts)</a></code></pre></div>
<pre><code>## [1] "integer"</code></pre>
-<div class="sourceCode" id="cb61"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb61-1" data-line-number="1"><span class="co"># Check the dimensions, each row is a gene, each column is a cell</span></a>
-<a class="sourceLine" id="cb61-2" data-line-number="2"><span class="kw">dim</span>(sc_example_counts)</a></code></pre></div>
+<div class="sourceCode" id="cb59"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb59-1" data-line-number="1"><span class="co"># Check the dimensions, each row is a gene, each column is a cell</span></a>
+<a class="sourceLine" id="cb59-2" data-line-number="2"><span class="kw">dim</span>(sc_example_counts)</a></code></pre></div>
<pre><code>## [1] 2000 40</code></pre>
-<div class="sourceCode" id="cb63"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb63-1" data-line-number="1"><span class="co"># Show the first few entries</span></a>
-<a class="sourceLine" id="cb63-2" data-line-number="2">sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</a></code></pre></div>
+<div class="sourceCode" id="cb61"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb61-1" data-line-number="1"><span class="co"># Show the first few entries</span></a>
+<a class="sourceLine" id="cb61-2" data-line-number="2">sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</a></code></pre></div>
<pre><code>## Cell_001 Cell_002 Cell_003 Cell_004 Cell_005
## Gene_0001 0 123 2 0 0
## Gene_0002 575 65 3 1561 2311
## Gene_0003 0 0 0 0 1213
## Gene_0004 0 1 0 0 0
## Gene_0005 0 0 11 0 0</code></pre>
-<div class="sourceCode" id="cb65"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb65-1" data-line-number="1">params <-<span class="st"> </span><span class="kw"><a href="../reference/splatEstimate.html">splatEstimate</a></span>(sc_example_counts)</a></code></pre></div>
-<pre><code>## NOTE: Library sizes have been found to be normally distributed instead of log-normal. You may want to check this is correct.</code></pre>
+<div class="sourceCode" id="cb63"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb63-1" data-line-number="1">params <-<span class="st"> </span><span class="kw"><a href="../reference/splatEstimate.html">splatEstimate</a></span>(sc_example_counts)</a></code></pre></div>
<p>Here we estimated parameters from a counts matrix but <code>splatEstimate</code> can also take a <code>SingleCellExperiment</code> object. The estimation process has the following steps:</p>
<ol style="list-style-type: decimal">
<li>Mean parameters are estimated by fitting a gamma distribution to the mean expression levels.</li>
@@ -483,7 +489,7 @@
<h1 class="hasAnchor">
<a href="#simulating-counts" class="anchor"></a>Simulating counts</h1>
<p>Once we have a set of parameters we are happy with we can use <code>splatSimulate</code> to simulate counts. If we want to make small adjustments to the parameters we can provide them as additional arguments, alternatively if we don’t supply any parameters the defaults will be used:</p>
-<div class="sourceCode" id="cb67"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb67-1" data-line-number="1">sim <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(params, <span class="dt">nGenes =</span> <span class="dv">1000</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb64"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb64-1" data-line-number="1">sim <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(params, <span class="dt">nGenes =</span> <span class="dv">1000</span>)</a></code></pre></div>
<pre><code>## Getting parameters...</code></pre>
<pre><code>## Creating simulation object...</code></pre>
<pre><code>## Simulating library sizes...</code></pre>
@@ -492,7 +498,7 @@
<pre><code>## Simulating counts..</code></pre>
<pre><code>## Simulating dropout (if needed)...</code></pre>
<pre><code>## Done!</code></pre>
-<div class="sourceCode" id="cb76"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb76-1" data-line-number="1">sim</a></code></pre></div>
+<div class="sourceCode" id="cb73"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb73-1" data-line-number="1">sim</a></code></pre></div>
<pre><code>## class: SingleCellExperiment
## dim: 1000 40
## metadata(1): Params
@@ -504,54 +510,54 @@
## reducedDimNames(0):
## spikeNames(0):</code></pre>
<p>Looking at the output of <code>splatSimulate</code> we can see that <code>sim</code> is <code>SingleCellExperiment</code> object with 1000 features (genes) and 40 samples (cells). The main part of this object is a features by samples matrix containing the simulated counts (accessed using <code>counts</code>), although it can also hold other expression measures such as FPKM or TPM. Additionaly a <code>SingleCellExperiment</code> contains phenotype information about each cell (accessed using <code>colData</code>) and feature information about each gene (accessed using <code>rowData</code>). Splatter uses these slots, as well as <code>assays</code>, to store information about the intermediate values of the simulation.</p>
-<div class="sourceCode" id="cb78"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb78-1" data-line-number="1"><span class="co"># Access the counts</span></a>
-<a class="sourceLine" id="cb78-2" data-line-number="2"><span class="kw">counts</span>(sim)[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</a></code></pre></div>
+<div class="sourceCode" id="cb75"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb75-1" data-line-number="1"><span class="co"># Access the counts</span></a>
+<a class="sourceLine" id="cb75-2" data-line-number="2"><span class="kw">counts</span>(sim)[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</a></code></pre></div>
<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
-## Gene1 0 0 0 0 0
-## Gene2 24 0 15 0 0
-## Gene3 0 112 0 2 0
-## Gene4 0 15 19 8 0
-## Gene5 0 119 0 0 0</code></pre>
-<div class="sourceCode" id="cb80"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb80-1" data-line-number="1"><span class="co"># Information about genes</span></a>
-<a class="sourceLine" id="cb80-2" data-line-number="2"><span class="kw">head</span>(<span class="kw">rowData</span>(sim))</a></code></pre></div>
+## Gene1 55 2 0 11 0
+## Gene2 1 2 0 0 0
+## Gene3 7 2 2 74 8
+## Gene4 0 69 6 0 114
+## Gene5 1 70 40 0 0</code></pre>
+<div class="sourceCode" id="cb77"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb77-1" data-line-number="1"><span class="co"># Information about genes</span></a>
+<a class="sourceLine" id="cb77-2" data-line-number="2"><span class="kw">head</span>(<span class="kw">rowData</span>(sim))</a></code></pre></div>
<pre><code>## DataFrame with 6 rows and 4 columns
-## Gene BaseGeneMean OutlierFactor GeneMean
-## <factor> <numeric> <numeric> <numeric>
-## 1 Gene1 0.0130414813167312 1 0.0130414813167312
-## 2 Gene2 8.22812161052673 1 8.22812161052673
-## 3 Gene3 94.0106124465794 1 94.0106124465794
-## 4 Gene4 463.408618692168 1 463.408618692168
-## 5 Gene5 8.17204397802014 1 8.17204397802014
-## 6 Gene6 82.8824018477604 1 82.8824018477604</code></pre>
-<div class="sourceCode" id="cb82"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb82-1" data-line-number="1"><span class="co"># Information about cells</span></a>
-<a class="sourceLine" id="cb82-2" data-line-number="2"><span class="kw">head</span>(<span class="kw">colData</span>(sim))</a></code></pre></div>
+## Gene BaseGeneMean OutlierFactor GeneMean
+## <factor> <numeric> <numeric> <numeric>
+## 1 Gene1 76.9025430673341 1 76.9025430673341
+## 2 Gene2 11.5038956210654 1 11.5038956210654
+## 3 Gene3 9.5216589952532 1 9.5216589952532
+## 4 Gene4 740.124978536434 1 740.124978536434
+## 5 Gene5 71.5386607136642 1 71.5386607136642
+## 6 Gene6 1.06151313409539 1 1.06151313409539</code></pre>
+<div class="sourceCode" id="cb79"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb79-1" data-line-number="1"><span class="co"># Information about cells</span></a>
+<a class="sourceLine" id="cb79-2" data-line-number="2"><span class="kw">head</span>(<span class="kw">colData</span>(sim))</a></code></pre></div>
<pre><code>## DataFrame with 6 rows and 3 columns
## Cell Batch ExpLibSize
## <factor> <character> <numeric>
-## Cell1 Cell1 Batch1 417797.914401539
-## Cell2 Cell2 Batch1 292966.340021102
-## Cell3 Cell3 Batch1 29202.3477378194
-## Cell4 Cell4 Batch1 307931.285977102
-## Cell5 Cell5 Batch1 291609.629194382
-## Cell6 Cell6 Batch1 580684.827308051</code></pre>
-<div class="sourceCode" id="cb84"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb84-1" data-line-number="1"><span class="co"># Gene by cell matrices</span></a>
-<a class="sourceLine" id="cb84-2" data-line-number="2"><span class="kw">names</span>(<span class="kw">assays</span>(sim))</a></code></pre></div>
+## Cell1 Cell1 Batch1 510286.263476612
+## Cell2 Cell2 Batch1 1202024.11389745
+## Cell3 Cell3 Batch1 183908.161529651
+## Cell4 Cell4 Batch1 154585.938029774
+## Cell5 Cell5 Batch1 619536.71187027
+## Cell6 Cell6 Batch1 266676.834832325</code></pre>
+<div class="sourceCode" id="cb81"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb81-1" data-line-number="1"><span class="co"># Gene by cell matrices</span></a>
+<a class="sourceLine" id="cb81-2" data-line-number="2"><span class="kw">names</span>(<span class="kw">assays</span>(sim))</a></code></pre></div>
<pre><code>## [1] "BatchCellMeans" "BaseCellMeans" "BCV" "CellMeans"
## [5] "TrueCounts" "counts"</code></pre>
-<div class="sourceCode" id="cb86"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb86-1" data-line-number="1"><span class="co"># Example of cell means matrix</span></a>
-<a class="sourceLine" id="cb86-2" data-line-number="2"><span class="kw">assays</span>(sim)<span class="op">$</span>CellMeans[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</a></code></pre></div>
-<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
-## Gene1 1.770411e-03 2.306051e-27 3.092778e-04 1.730713e-38 3.735798e-35
-## Gene2 2.507370e+01 2.388855e-19 1.629559e+01 1.405443e-05 4.289045e-03
-## Gene3 5.586177e-06 1.059315e+02 1.635766e-07 1.327532e+00 1.695889e-14
-## Gene4 1.129532e+00 1.036317e+01 1.679162e+01 8.609940e+00 5.195456e-11
-## Gene5 3.468714e-02 1.040199e+02 1.169722e-03 1.047193e-01 2.080234e-03</code></pre>
+<div class="sourceCode" id="cb83"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb83-1" data-line-number="1"><span class="co"># Example of cell means matrix</span></a>
+<a class="sourceLine" id="cb83-2" data-line-number="2"><span class="kw">assays</span>(sim)<span class="op">$</span>CellMeans[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</a></code></pre></div>
+<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
+## Gene1 5.333124e+01 2.598563 1.529988e-01 11.676286605 3.982157e-03
+## Gene2 7.665400e-01 7.586450 1.614969e-25 0.372529598 6.068763e-03
+## Gene3 6.121509e+00 1.784225 6.033250e+00 74.377980371 6.435478e+00
+## Gene4 8.789318e-06 69.991629 7.918106e+00 0.026909108 1.193434e+02
+## Gene5 8.940025e-02 94.814168 3.921096e+01 0.008752188 1.123261e-01</code></pre>
<p>An additional (big) advantage of outputting a <code>SingleCellExperiment</code> is that we get immediate access to other analysis packages, such as the plotting functions in <code>scater</code>. For example we can make a PCA plot:</p>
-<div class="sourceCode" id="cb88"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb88-1" data-line-number="1"><span class="co"># Use scater to calculate logcounts</span></a>
-<a class="sourceLine" id="cb88-2" data-line-number="2">sim <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim)</a></code></pre></div>
+<div class="sourceCode" id="cb85"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb85-1" data-line-number="1"><span class="co"># Use scater to calculate logcounts</span></a>
+<a class="sourceLine" id="cb85-2" data-line-number="2">sim <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim)</a></code></pre></div>
<pre><code>## Warning in .local(object, ...): using library sizes as size factors</code></pre>
-<div class="sourceCode" id="cb90"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb90-1" data-line-number="1"><span class="co"># Plot PCA</span></a>
-<a class="sourceLine" id="cb90-2" data-line-number="2"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim)</a></code></pre></div>
+<div class="sourceCode" id="cb87"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb87-1" data-line-number="1"><span class="co"># Plot PCA</span></a>
+<a class="sourceLine" id="cb87-2" data-line-number="2"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim)</a></code></pre></div>
<p><img src="splatter_files/figure-html/pca-1.png" width="576" style="display: block; margin: auto;"></p>
<p>(<strong>NOTE:</strong> Your values and plots may look different as the simulation is random and produces different results each time it is run.)</p>
<p>For more details about the <code>SingleCellExperiment</code> object refer to the [vignette] <a href="https://bioconductor.org/packages/devel/bioc/vignettes/SingleCellExperiment/inst/doc/intro.html">SCE-vignette</a>. For information about what you can do with <code>scater</code> refer to the <code>scater</code> documentation and <a href="https://bioconductor.org/packages/release/bioc/vignettes/scater/inst/doc/vignette.html">vignette</a>.</p>
@@ -609,11 +615,11 @@
<a href="#simulating-groups" class="anchor"></a>Simulating groups</h2>
<p>So far we have only simulated a single population of cells but often we are interested in investigating a mixed population of cells and looking to see what cell types are present or what differences there are between them. Splatter is able to simulate these situations by changing the <code>method</code> argument Here we are going to simulate two groups, by specifying the <code>group.prob</code> parameter and setting the <code>method</code> parameter to <code>"groups"</code>:</p>
<p>(<strong>NOTE:</strong> We have also set the <code>verbose</code> argument to <code>FALSE</code> to stop Splatter printing progress messages.)</p>
-<div class="sourceCode" id="cb91"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb91-1" data-line-number="1">sim.groups <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">group.prob =</span> <span class="kw">c</span>(<span class="fl">0.5</span>, <span class="fl">0.5</span>), <span class="dt">method =</span> <span class="st">"groups"</span>,</a>
-<a class="sourceLine" id="cb91-2" data-line-number="2"> <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb91-3" data-line-number="3">sim.groups <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.groups)</a></code></pre></div>
+<div class="sourceCode" id="cb88"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb88-1" data-line-number="1">sim.groups <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">group.prob =</span> <span class="kw">c</span>(<span class="fl">0.5</span>, <span class="fl">0.5</span>), <span class="dt">method =</span> <span class="st">"groups"</span>,</a>
+<a class="sourceLine" id="cb88-2" data-line-number="2"> <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb88-3" data-line-number="3">sim.groups <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.groups)</a></code></pre></div>
<pre><code>## Warning in .local(object, ...): using library sizes as size factors</code></pre>
-<div class="sourceCode" id="cb93"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb93-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim.groups, <span class="dt">colour_by =</span> <span class="st">"Group"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb90"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb90-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim.groups, <span class="dt">colour_by =</span> <span class="st">"Group"</span>)</a></code></pre></div>
<p><img src="splatter_files/figure-html/groups-1.png" width="576" style="display: block; margin: auto;"></p>
<p>As we have set both the group probabilites to 0.5 we should get approximately equal numbers of cells in each group (around 50 in this case). If we wanted uneven groups we could set <code>group.prob</code> to any set of probabilites that sum to 1.</p>
</div>
@@ -621,10 +627,10 @@
<h2 class="hasAnchor">
<a href="#simulating-paths" class="anchor"></a>Simulating paths</h2>
<p>The other situation that is often of interest is a differentiation process where one cell type is changing into another. Splatter approximates this process by simulating a series of steps between two groups and randomly assigning each cell to a step. We can create this kind of simulation using the <code>"paths"</code> method.</p>
-<div class="sourceCode" id="cb94"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb94-1" data-line-number="1">sim.paths <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">method =</span> <span class="st">"paths"</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb94-2" data-line-number="2">sim.paths <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.paths)</a></code></pre></div>
+<div class="sourceCode" id="cb91"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb91-1" data-line-number="1">sim.paths <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">method =</span> <span class="st">"paths"</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb91-2" data-line-number="2">sim.paths <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.paths)</a></code></pre></div>
<pre><code>## Warning in .local(object, ...): using library sizes as size factors</code></pre>
-<div class="sourceCode" id="cb96"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb96-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim.paths, <span class="dt">colour_by =</span> <span class="st">"Step"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb93"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb93-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim.paths, <span class="dt">colour_by =</span> <span class="st">"Step"</span>)</a></code></pre></div>
<p><img src="splatter_files/figure-html/paths-1.png" width="576" style="display: block; margin: auto;"></p>
<p>Here the colours represent the “step†of each cell or how far along the differentiation path it is. We can see that the cells with dark colours are more similar to the originating cell type and the light coloured cells are closer to the final, differentiated, cell type. By setting additional parameters it is possible to simulate more complex process (for example multiple mature cell types from a single progenitor).</p>
</div>
@@ -632,17 +638,17 @@
<h2 class="hasAnchor">
<a href="#batch-effects" class="anchor"></a>Batch effects</h2>
<p>Another factor that is important in the analysis of any sequencing experiment are batch effects, technical variation that is common to a set of samples processed at the same time. We apply batch effects by telling Splatter how many cells are in each batch:</p>
-<div class="sourceCode" id="cb97"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb97-1" data-line-number="1">sim.batches <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">batchCells =</span> <span class="kw">c</span>(<span class="dv">50</span>, <span class="dv">50</span>), <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb97-2" data-line-number="2">sim.batches <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.batches)</a></code></pre></div>
+<div class="sourceCode" id="cb94"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb94-1" data-line-number="1">sim.batches <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">batchCells =</span> <span class="kw">c</span>(<span class="dv">50</span>, <span class="dv">50</span>), <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb94-2" data-line-number="2">sim.batches <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.batches)</a></code></pre></div>
<pre><code>## Warning in .local(object, ...): using library sizes as size factors</code></pre>
-<div class="sourceCode" id="cb99"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb99-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim.batches, <span class="dt">colour_by =</span> <span class="st">"Batch"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb96"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb96-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim.batches, <span class="dt">colour_by =</span> <span class="st">"Batch"</span>)</a></code></pre></div>
<p><img src="splatter_files/figure-html/batches-1.png" width="576" style="display: block; margin: auto;"></p>
<p>This looks at lot like when we simulated groups and that is because the process is very similar. The difference is that batch effects are applied to all genes, not just those that are differentially expressed, and the effects are usually smaller. By combining groups and batches we can simulate both unwanted variation that we aren’t interested in (batch) and the wanted variation we are looking for (group):</p>
-<div class="sourceCode" id="cb100"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb100-1" data-line-number="1">sim.groups <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">batchCells =</span> <span class="kw">c</span>(<span class="dv">50</span>, <span class="dv">50</span>), <span class="dt">group.prob =</span> <span class="kw">c</span>(<span class="fl">0.5</span>, <span class="fl">0.5</span>),</a>
-<a class="sourceLine" id="cb100-2" data-line-number="2"> <span class="dt">method =</span> <span class="st">"groups"</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb100-3" data-line-number="3">sim.groups <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.groups)</a></code></pre></div>
+<div class="sourceCode" id="cb97"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb97-1" data-line-number="1">sim.groups <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">batchCells =</span> <span class="kw">c</span>(<span class="dv">50</span>, <span class="dv">50</span>), <span class="dt">group.prob =</span> <span class="kw">c</span>(<span class="fl">0.5</span>, <span class="fl">0.5</span>),</a>
+<a class="sourceLine" id="cb97-2" data-line-number="2"> <span class="dt">method =</span> <span class="st">"groups"</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb97-3" data-line-number="3">sim.groups <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.groups)</a></code></pre></div>
<pre><code>## Warning in .local(object, ...): using library sizes as size factors</code></pre>
-<div class="sourceCode" id="cb102"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb102-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim.groups, <span class="dt">shape_by =</span> <span class="st">"Batch"</span>, <span class="dt">colour_by =</span> <span class="st">"Group"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb99"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb99-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim.groups, <span class="dt">shape_by =</span> <span class="st">"Batch"</span>, <span class="dt">colour_by =</span> <span class="st">"Group"</span>)</a></code></pre></div>
<p><img src="splatter_files/figure-html/batch-groups-1.png" width="576" style="display: block; margin: auto;"></p>
<p>Here we see that the effects of the group (first component) are stronger than the batch effects (second component) but by adjusting the parameters we could made the batch effects dominate.</p>
</div>
@@ -656,7 +662,7 @@
<h1 class="hasAnchor">
<a href="#other-simulations" class="anchor"></a>Other simulations</h1>
<p>As well as it’s own Splat simulation method the Splatter package contains implementations of other single-cell RNA-seq simulations that have been published or wrappers around simulations included in other packages. To see all the available simulations run the <code><a href="../reference/listSims.html">listSims()</a></code> function:</p>
-<div class="sourceCode" id="cb103"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb103-1" data-line-number="1"><span class="kw"><a href="../reference/listSims.html">listSims</a></span>()</a></code></pre></div>
+<div class="sourceCode" id="cb100"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb100-1" data-line-number="1"><span class="kw"><a href="../reference/listSims.html">listSims</a></span>()</a></code></pre></div>
<pre><code>## Splatter currently contains 13 simulations
##
## Splat (splat)
@@ -711,7 +717,7 @@
## DOI: 10.1093/nar/gkx1113 GitHub: cran/SparseDC
## The SparseDC simulation simulates a set of clusters across two conditions, where some clusters may be present in only one condition.</code></pre>
<p>(or more conveniently for the vignette as a table)</p>
-<div class="sourceCode" id="cb105"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb105-1" data-line-number="1">knitr<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/knitr/topics/kable">kable</a></span>(<span class="kw"><a href="../reference/listSims.html">listSims</a></span>(<span class="dt">print =</span> <span class="ot">FALSE</span>))</a></code></pre></div>
+<div class="sourceCode" id="cb102"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb102-1" data-line-number="1">knitr<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/knitr/topics/kable">kable</a></span>(<span class="kw"><a href="../reference/listSims.html">listSims</a></span>(<span class="dt">print =</span> <span class="ot">FALSE</span>))</a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="left">Name</th>
@@ -820,67 +826,67 @@
<h1 class="hasAnchor">
<a href="#other-expression-values" class="anchor"></a>Other expression values</h1>
<p>Splatter is designed to simulate count data but some analysis methods expect other expression values, particularly length-normalised values such as TPM or FPKM. The <code>scater</code> package has functions for adding these values to a <code>SingleCellExperiment</code> object but they require a length for each gene. The <code>addGeneLengths</code> function can be used to simulate these lengths:</p>
-<div class="sourceCode" id="cb106"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb106-1" data-line-number="1">sim <-<span class="st"> </span><span class="kw"><a href="../reference/simpleSimulate.html">simpleSimulate</a></span>(<span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb106-2" data-line-number="2">sim <-<span class="st"> </span><span class="kw"><a href="../reference/addGeneLengths.html">addGeneLengths</a></span>(sim)</a>
-<a class="sourceLine" id="cb106-3" data-line-number="3"><span class="kw">head</span>(<span class="kw">rowData</span>(sim))</a></code></pre></div>
+<div class="sourceCode" id="cb103"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb103-1" data-line-number="1">sim <-<span class="st"> </span><span class="kw"><a href="../reference/simpleSimulate.html">simpleSimulate</a></span>(<span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb103-2" data-line-number="2">sim <-<span class="st"> </span><span class="kw"><a href="../reference/addGeneLengths.html">addGeneLengths</a></span>(sim)</a>
+<a class="sourceLine" id="cb103-3" data-line-number="3"><span class="kw">head</span>(<span class="kw">rowData</span>(sim))</a></code></pre></div>
<pre><code>## DataFrame with 6 rows and 3 columns
-## Gene GeneMean Length
-## <factor> <numeric> <numeric>
-## 1 Gene1 0.31504131758053 1118
-## 2 Gene2 0.00417585217082588 2098
-## 3 Gene3 0.373634067284232 3416
-## 4 Gene4 0.310092742796264 807
-## 5 Gene5 2.88627905029782 4492
-## 6 Gene6 0.610061028603659 7264</code></pre>
+## Gene GeneMean Length
+## <factor> <numeric> <numeric>
+## 1 Gene1 0.0489642776646331 1937
+## 2 Gene2 3.20462567086451 2196
+## 3 Gene3 0.364784855489904 9883
+## 4 Gene4 0.110583350422224 1810
+## 5 Gene5 0.661617770742839 1177
+## 6 Gene6 0.101683292027918 2012</code></pre>
<p>We can then use <code>scater</code> to calculate TPM:</p>
-<div class="sourceCode" id="cb108"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb108-1" data-line-number="1"><span class="kw">tpm</span>(sim) <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/calculateTPM">calculateTPM</a></span>(sim, <span class="kw">rowData</span>(sim)<span class="op">$</span>Length)</a>
-<a class="sourceLine" id="cb108-2" data-line-number="2"><span class="kw">tpm</span>(sim)[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</a></code></pre></div>
-<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
-## Gene1 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
-## Gene2 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
-## Gene3 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
-## Gene4 0.09404655 0.00000000 0.00000000 0.00000000 0.09265421
-## Gene5 0.03379144 0.01683821 0.03369681 0.01712314 0.08322790</code></pre>
+<div class="sourceCode" id="cb105"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb105-1" data-line-number="1"><span class="kw">tpm</span>(sim) <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/calculateTPM">calculateTPM</a></span>(sim, <span class="kw">rowData</span>(sim)<span class="op">$</span>Length)</a>
+<a class="sourceLine" id="cb105-2" data-line-number="2"><span class="kw">tpm</span>(sim)[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</a></code></pre></div>
+<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
+## Gene1 0.0000000 0.000000000 0.00000000 0.000000000 0.000000000
+## Gene2 0.2338332 0.033654084 0.09984799 0.000000000 0.066541011
+## Gene3 0.0000000 0.007477929 0.00000000 0.007379757 0.007392698
+## Gene4 0.0000000 0.000000000 0.04038051 0.000000000 0.000000000
+## Gene5 0.0000000 0.062790457 0.06209748 0.247864539 0.000000000</code></pre>
<p>The default method used by <code>addGeneLengths</code> to simulate lengths is to generate values from a log-normal distribution which are then rounded to give an integer length. The parameters for this distribution are based on human protein coding genes but can be adjusted if needed (for example for other species). Alternatively lengths can be sampled from a provided vector (see <code><a href="../reference/addGeneLengths.html">?addGeneLengths</a></code> for details and an example).</p>
</div>
<div id="comparing-simulations-and-real-data" class="section level1">
<h1 class="hasAnchor">
<a href="#comparing-simulations-and-real-data" class="anchor"></a>Comparing simulations and real data</h1>
<p>One thing you might like to do after simulating data is to compare it to a real dataset, or compare simulations with different parameters or models. Splatter provides a function <code>compareSCEs</code> that aims to make these comparisons easier. As the name suggests this function takes a list of <code>SingleCellExperiment</code> objects, combines the datasets and produces some plots comparing them. Let’s make two small simulations and see how they compare.</p>
-<div class="sourceCode" id="cb110"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb110-1" data-line-number="1">sim1 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">nGenes =</span> <span class="dv">1000</span>, <span class="dt">batchCells =</span> <span class="dv">20</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb110-2" data-line-number="2">sim2 <-<span class="st"> </span><span class="kw"><a href="../reference/simpleSimulate.html">simpleSimulate</a></span>(<span class="dt">nGenes =</span> <span class="dv">1000</span>, <span class="dt">nCells =</span> <span class="dv">20</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb110-3" data-line-number="3">comparison <-<span class="st"> </span><span class="kw"><a href="../reference/compareSCEs.html">compareSCEs</a></span>(<span class="kw">list</span>(<span class="dt">Splat =</span> sim1, <span class="dt">Simple =</span> sim2))</a></code></pre></div>
+<div class="sourceCode" id="cb107"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb107-1" data-line-number="1">sim1 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">nGenes =</span> <span class="dv">1000</span>, <span class="dt">batchCells =</span> <span class="dv">20</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb107-2" data-line-number="2">sim2 <-<span class="st"> </span><span class="kw"><a href="../reference/simpleSimulate.html">simpleSimulate</a></span>(<span class="dt">nGenes =</span> <span class="dv">1000</span>, <span class="dt">nCells =</span> <span class="dv">20</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb107-3" data-line-number="3">comparison <-<span class="st"> </span><span class="kw"><a href="../reference/compareSCEs.html">compareSCEs</a></span>(<span class="kw">list</span>(<span class="dt">Splat =</span> sim1, <span class="dt">Simple =</span> sim2))</a></code></pre></div>
<pre><code>## Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.
## Old names are currently maintained for back-compatibility, but may be removed in future releases.
## Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.
## Old names are currently maintained for back-compatibility, but may be removed in future releases.</code></pre>
-<div class="sourceCode" id="cb112"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb112-1" data-line-number="1"><span class="kw">names</span>(comparison)</a></code></pre></div>
+<div class="sourceCode" id="cb109"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb109-1" data-line-number="1"><span class="kw">names</span>(comparison)</a></code></pre></div>
<pre><code>## [1] "FeatureData" "PhenoData" "Plots"</code></pre>
-<div class="sourceCode" id="cb114"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb114-1" data-line-number="1"><span class="kw">names</span>(comparison<span class="op">$</span>Plots)</a></code></pre></div>
+<div class="sourceCode" id="cb111"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb111-1" data-line-number="1"><span class="kw">names</span>(comparison<span class="op">$</span>Plots)</a></code></pre></div>
<pre><code>## [1] "Means" "Variances" "MeanVar" "LibrarySizes"
## [5] "ZerosGene" "ZerosCell" "MeanZeros"</code></pre>
<p>The returned list has three items. The first two are the combined datasets by gene (<code>FeatureData</code>) and by cell (<code>PhenoData</code>) and the third contains some comparison plots (produced using <code>ggplot2</code>), for example a plot of the distribution of means:</p>
-<div class="sourceCode" id="cb116"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb116-1" data-line-number="1">comparison<span class="op">$</span>Plots<span class="op">$</span>Means</a></code></pre></div>
+<div class="sourceCode" id="cb113"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb113-1" data-line-number="1">comparison<span class="op">$</span>Plots<span class="op">$</span>Means</a></code></pre></div>
<p><img src="splatter_files/figure-html/comparison-means-1.png" width="576" style="display: block; margin: auto;"></p>
<p>These are only a few of the plots you might want to consider but it should be easy to make more using the returned data. For example, we could plot the number of expressed genes against the library size:</p>
-<div class="sourceCode" id="cb117"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb117-1" data-line-number="1"><span class="kw">library</span>(<span class="st">"ggplot2"</span>)</a>
-<a class="sourceLine" id="cb117-2" data-line-number="2"><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>(comparison<span class="op">$</span>PhenoData,</a>
-<a class="sourceLine" id="cb117-3" data-line-number="3"> <span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>(<span class="dt">x =</span> total_counts, <span class="dt">y =</span> total_features, <span class="dt">colour =</span> Dataset)) <span class="op">+</span></a>
-<a class="sourceLine" id="cb117-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_point">geom_point</a></span>()</a></code></pre></div>
+<div class="sourceCode" id="cb114"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb114-1" data-line-number="1"><span class="kw">library</span>(<span class="st">"ggplot2"</span>)</a>
+<a class="sourceLine" id="cb114-2" data-line-number="2"><span class="kw"><a href="ggplot2.tidyverse.org/reference/ggplot.html">ggplot</a></span>(comparison<span class="op">$</span>PhenoData,</a>
+<a class="sourceLine" id="cb114-3" data-line-number="3"> <span class="kw"><a href="ggplot2.tidyverse.org/reference/aes.html">aes</a></span>(<span class="dt">x =</span> total_counts, <span class="dt">y =</span> total_features_by_counts, <span class="dt">colour =</span> Dataset)) <span class="op">+</span></a>
+<a class="sourceLine" id="cb114-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="ggplot2.tidyverse.org/reference/geom_point.html">geom_point</a></span>()</a></code></pre></div>
<p><img src="splatter_files/figure-html/comparison-libsize-features-1.png" width="576" style="display: block; margin: auto;"></p>
<div id="comparing-differences" class="section level2">
<h2 class="hasAnchor">
<a href="#comparing-differences" class="anchor"></a>Comparing differences</h2>
<p>Sometimes instead of visually comparing datasets it may be more interesting to look at the differences between them. We can do this using the <code>diffSCEs</code> function. Similar to <code>compareSCEs</code> this function takes a list of <code>SingleCellExperiment</code> objects but now we also specify one to be a reference. A series of similar plots are returned but instead of showing the overall distributions they demonstrate differences from the reference.</p>
-<div class="sourceCode" id="cb118"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb118-1" data-line-number="1">difference <-<span class="st"> </span><span class="kw"><a href="../reference/diffSCEs.html">diffSCEs</a></span>(<span class="kw">list</span>(<span class="dt">Splat =</span> sim1, <span class="dt">Simple =</span> sim2), <span class="dt">ref =</span> <span class="st">"Simple"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb115"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb115-1" data-line-number="1">difference <-<span class="st"> </span><span class="kw"><a href="../reference/diffSCEs.html">diffSCEs</a></span>(<span class="kw">list</span>(<span class="dt">Splat =</span> sim1, <span class="dt">Simple =</span> sim2), <span class="dt">ref =</span> <span class="st">"Simple"</span>)</a></code></pre></div>
<pre><code>## Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.
## Old names are currently maintained for back-compatibility, but may be removed in future releases.
## Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.
## Old names are currently maintained for back-compatibility, but may be removed in future releases.</code></pre>
-<div class="sourceCode" id="cb120"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb120-1" data-line-number="1">difference<span class="op">$</span>Plots<span class="op">$</span>Means</a></code></pre></div>
+<div class="sourceCode" id="cb117"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb117-1" data-line-number="1">difference<span class="op">$</span>Plots<span class="op">$</span>Means</a></code></pre></div>
<p><img src="splatter_files/figure-html/difference-1.png" width="576" style="display: block; margin: auto;"></p>
<p>We also get a series of Quantile-Quantile plot that can be used to compare distributions.</p>
-<div class="sourceCode" id="cb121"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb121-1" data-line-number="1">difference<span class="op">$</span>QQPlots<span class="op">$</span>Means</a></code></pre></div>
+<div class="sourceCode" id="cb118"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb118-1" data-line-number="1">difference<span class="op">$</span>QQPlots<span class="op">$</span>Means</a></code></pre></div>
<p><img src="splatter_files/figure-html/difference-qq-1.png" width="576" style="display: block; margin: auto;"></p>
</div>
<div id="making-panels" class="section level2">
@@ -888,22 +894,22 @@
<a href="#making-panels" class="anchor"></a>Making panels</h2>
<p>Each of these comparisons makes several plots which can be a lot to look at. To make this easier, or to produce figures for publications, you can make use of the functions <code>makeCompPanel</code>, <code>makeDiffPanel</code> and <code>makeOverallPanel</code>.</p>
<p>These functions combine the plots into a single panel using the <code>cowplot</code> package. The panels can be quite large and hard to view (for example in RStudio’s plot viewer) so it can be better to output the panels and view them separately. Luckily <code>cowplot</code> provides a convenient function for saving the images. Here are some suggested parameters for outputting each of the panels:</p>
-<div class="sourceCode" id="cb122"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb122-1" data-line-number="1"><span class="co"># This code is just an example and is not run</span></a>
-<a class="sourceLine" id="cb122-2" data-line-number="2">panel <-<span class="st"> </span><span class="kw"><a href="../reference/makeCompPanel.html">makeCompPanel</a></span>(comparison)</a>
-<a class="sourceLine" id="cb122-3" data-line-number="3">cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/cowplot/topics/save_plot">save_plot</a></span>(<span class="st">"comp_panel.png"</span>, panel, <span class="dt">nrow =</span> <span class="dv">4</span>, <span class="dt">ncol =</span> <span class="dv">3</span>)</a>
-<a class="sourceLine" id="cb122-4" data-line-number="4"></a>
-<a class="sourceLine" id="cb122-5" data-line-number="5">panel <-<span class="st"> </span><span class="kw"><a href="../reference/makeDiffPanel.html">makeDiffPanel</a></span>(difference)</a>
-<a class="sourceLine" id="cb122-6" data-line-number="6">cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/cowplot/topics/save_plot">save_plot</a></span>(<span class="st">"diff_panel.png"</span>, panel, <span class="dt">nrow =</span> <span class="dv">3</span>, <span class="dt">ncol =</span> <span class="dv">5</span>)</a>
-<a class="sourceLine" id="cb122-7" data-line-number="7"></a>
-<a class="sourceLine" id="cb122-8" data-line-number="8">panel <-<span class="st"> </span><span class="kw"><a href="../reference/makeOverallPanel.html">makeOverallPanel</a></span>(comparison, difference)</a>
-<a class="sourceLine" id="cb122-9" data-line-number="9">cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/cowplot/topics/save_plot">save_plot</a></span>(<span class="st">"overall_panel.png"</span>, panel, <span class="dt">ncol =</span> <span class="dv">4</span>, <span class="dt">nrow =</span> <span class="dv">7</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb119"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb119-1" data-line-number="1"><span class="co"># This code is just an example and is not run</span></a>
+<a class="sourceLine" id="cb119-2" data-line-number="2">panel <-<span class="st"> </span><span class="kw"><a href="../reference/makeCompPanel.html">makeCompPanel</a></span>(comparison)</a>
+<a class="sourceLine" id="cb119-3" data-line-number="3">cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/cowplot/topics/save_plot">save_plot</a></span>(<span class="st">"comp_panel.png"</span>, panel, <span class="dt">nrow =</span> <span class="dv">4</span>, <span class="dt">ncol =</span> <span class="dv">3</span>)</a>
+<a class="sourceLine" id="cb119-4" data-line-number="4"></a>
+<a class="sourceLine" id="cb119-5" data-line-number="5">panel <-<span class="st"> </span><span class="kw"><a href="../reference/makeDiffPanel.html">makeDiffPanel</a></span>(difference)</a>
+<a class="sourceLine" id="cb119-6" data-line-number="6">cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/cowplot/topics/save_plot">save_plot</a></span>(<span class="st">"diff_panel.png"</span>, panel, <span class="dt">nrow =</span> <span class="dv">3</span>, <span class="dt">ncol =</span> <span class="dv">5</span>)</a>
+<a class="sourceLine" id="cb119-7" data-line-number="7"></a>
+<a class="sourceLine" id="cb119-8" data-line-number="8">panel <-<span class="st"> </span><span class="kw"><a href="../reference/makeOverallPanel.html">makeOverallPanel</a></span>(comparison, difference)</a>
+<a class="sourceLine" id="cb119-9" data-line-number="9">cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/cowplot/topics/save_plot">save_plot</a></span>(<span class="st">"overall_panel.png"</span>, panel, <span class="dt">ncol =</span> <span class="dv">4</span>, <span class="dt">nrow =</span> <span class="dv">7</span>)</a></code></pre></div>
</div>
</div>
<div id="citing-splatter" class="section level1">
<h1 class="hasAnchor">
<a href="#citing-splatter" class="anchor"></a>Citing Splatter</h1>
<p>If you use Splatter in your work please cite our paper:</p>
-<div class="sourceCode" id="cb123"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb123-1" data-line-number="1"><span class="kw">citation</span>(<span class="st">"splatter"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb120"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb120-1" data-line-number="1"><span class="kw">citation</span>(<span class="st">"splatter"</span>)</a></code></pre></div>
<pre><code>##
## Zappia L, Phipson B, Oshlack A. Splatter: Simulation of
## single-cell RNA sequencing data. Genome Biology. 2017;
@@ -923,8 +929,8 @@
<div id="session-information" class="section level1 unnumbered">
<h1 class="hasAnchor">
<a href="#session-information" class="anchor"></a>Session information</h1>
-<div class="sourceCode" id="cb125"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb125-1" data-line-number="1"><span class="kw">sessionInfo</span>()</a></code></pre></div>
-<pre><code>## R version 3.5.0 (2018-04-23)
+<div class="sourceCode" id="cb122"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb122-1" data-line-number="1"><span class="kw">sessionInfo</span>()</a></code></pre></div>
+<pre><code>## R version 3.5.1 (2018-07-02)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Sierra 10.12.6
##
@@ -940,52 +946,58 @@
## [8] methods base
##
## other attached packages:
-## [1] scater_1.8.0 ggplot2_2.2.1
-## [3] splatter_1.4.0 SingleCellExperiment_1.2.0
-## [5] SummarizedExperiment_1.10.0 DelayedArray_0.6.0
-## [7] BiocParallel_1.14.0 matrixStats_0.53.1
-## [9] Biobase_2.40.0 GenomicRanges_1.32.0
-## [11] GenomeInfoDb_1.16.0 IRanges_2.14.0
-## [13] S4Vectors_0.18.0 BiocGenerics_0.26.0
+## [1] scater_1.8.4 ggplot2_3.0.0
+## [3] splatter_1.4.3 SingleCellExperiment_1.2.0
+## [5] SummarizedExperiment_1.10.1 DelayedArray_0.6.5
+## [7] BiocParallel_1.14.2 matrixStats_0.54.0
+## [9] Biobase_2.40.0 GenomicRanges_1.32.6
+## [11] GenomeInfoDb_1.16.0 IRanges_2.14.11
+## [13] S4Vectors_0.18.3 BiocGenerics_0.26.0
+## [15] BiocStyle_2.8.2
##
## loaded via a namespace (and not attached):
-## [1] viridis_0.5.1 edgeR_3.22.0
-## [3] splines_3.5.0 viridisLite_0.3.0
-## [5] DelayedMatrixStats_1.2.0 shiny_1.0.5
-## [7] assertthat_0.2.0 highr_0.6
-## [9] sp_1.2-7 GenomeInfoDbData_1.1.0
-## [11] vipor_0.4.5 yaml_2.1.19
-## [13] pillar_1.2.2 backports_1.1.2
-## [15] lattice_0.20-35 glue_1.2.0
-## [17] limma_3.36.0 digest_0.6.15
-## [19] promises_1.0.1 XVector_0.20.0
-## [21] checkmate_1.8.6 colorspace_1.3-2
-## [23] cowplot_0.9.2 htmltools_0.3.6
-## [25] httpuv_1.4.1 Matrix_1.2-14
-## [27] plyr_1.8.4 pkgconfig_2.0.1
-## [29] zlibbioc_1.26.0 xtable_1.8-2
-## [31] scales_0.5.0 later_0.7.2
-## [33] tibble_1.4.2 lazyeval_0.2.1
-## [35] crayon_1.3.4 survival_2.42-3
-## [37] magrittr_1.5 mime_0.5
-## [39] evaluate_0.10.1 MASS_7.3-50
-## [41] beeswarm_0.2.3 shinydashboard_0.7.0
-## [43] tools_3.5.0 fitdistrplus_1.0-9
-## [45] data.table_1.11.0 stringr_1.3.0
-## [47] Rhdf5lib_1.2.0 munsell_0.4.3
-## [49] locfit_1.5-9.1 bindrcpp_0.2.2
-## [51] akima_0.6-2 compiler_3.5.0
-## [53] rlang_0.2.0 rhdf5_2.24.0
-## [55] grid_3.5.0 RCurl_1.95-4.10
-## [57] tximport_1.8.0 rjson_0.2.15
-## [59] labeling_0.3 bitops_1.0-6
-## [61] rmarkdown_1.9 gtable_0.2.0
-## [63] reshape2_1.4.3 R6_2.2.2
-## [65] gridExtra_2.3 knitr_1.20
-## [67] dplyr_0.7.4 bindr_0.1.1
-## [69] rprojroot_1.3-2 stringi_1.1.7
-## [71] ggbeeswarm_0.6.0 Rcpp_0.12.16</code></pre>
-</div>
+## [1] bitops_1.0-6 fs_1.2.6
+## [3] rprojroot_1.3-2 tools_3.5.1
+## [5] backports_1.1.2 R6_2.2.2
+## [7] vipor_0.4.5 lazyeval_0.2.1
+## [9] colorspace_1.3-2 sp_1.3-1
+## [11] withr_2.1.2 tidyselect_0.2.4
+## [13] gridExtra_2.3 compiler_3.5.1
+## [15] xml2_1.2.0 desc_1.2.0
+## [17] labeling_0.3 bookdown_0.7
+## [19] scales_1.0.0 checkmate_1.8.6
+## [21] pkgdown_1.1.0 commonmark_1.5
+## [23] stringr_1.3.1 digest_0.6.16
+## [25] rmarkdown_1.10 XVector_0.20.0
+## [27] pkgconfig_2.0.2 htmltools_0.3.6
+## [29] akima_0.6-2 highr_0.7
+## [31] limma_3.36.3 rlang_0.2.2
+## [33] shiny_1.1.0 DelayedMatrixStats_1.2.0
+## [35] bindr_0.1.1 dplyr_0.7.6
+## [37] RCurl_1.95-4.11 magrittr_1.5
+## [39] GenomeInfoDbData_1.1.0 Matrix_1.2-14
+## [41] Rcpp_0.12.18 ggbeeswarm_0.6.0
+## [43] munsell_0.5.0 Rhdf5lib_1.2.1
+## [45] viridis_0.5.1 stringi_1.2.4
+## [47] yaml_2.2.0 edgeR_3.22.3
+## [49] MASS_7.3-51 zlibbioc_1.26.0
+## [51] rhdf5_2.24.0 plyr_1.8.4
+## [53] grid_3.5.1 promises_1.0.1
+## [55] shinydashboard_0.7.0 crayon_1.3.4
+## [57] lattice_0.20-35 cowplot_0.9.3
+## [59] splines_3.5.1 locfit_1.5-9.1
+## [61] knitr_1.20 pillar_1.3.0
+## [63] rjson_0.2.20 reshape2_1.4.3
+## [65] glue_1.3.0 evaluate_0.11
+## [67] data.table_1.11.4 httpuv_1.4.5
+## [69] gtable_0.2.0 purrr_0.2.5
+## [71] assertthat_0.2.0 xfun_0.3
+## [73] mime_0.5 xtable_1.8-3
+## [75] roxygen2_6.1.0 later_0.7.4
+## [77] survival_2.42-6 viridisLite_0.3.0
+## [79] tibble_1.4.2 beeswarm_0.2.3
+## [81] memoise_1.1.0 tximport_1.8.0
+## [83] bindrcpp_0.2.2 fitdistrplus_1.0-9</code></pre>
</div>
</div>
@@ -1043,5 +1055,7 @@
</footer>
</div>
+
+
</body>
</html>
diff --git a/docs/articles/splatter_files/figure-html/batch-groups-1.png b/docs/articles/splatter_files/figure-html/batch-groups-1.png
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diff --git a/docs/articles/splatter_files/figure-html/groups-1.png b/docs/articles/splatter_files/figure-html/groups-1.png
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diff --git a/docs/articles/splatter_files/figure-html/paths-1.png b/docs/articles/splatter_files/figure-html/paths-1.png
index 95c94577508e394d8a557772283b5dfbd93eb89e..d13dc6196bd0ba01be8f4539abc0074daa75b87a 100644
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diff --git a/docs/articles/splatter_files/figure-html/pca-1.png b/docs/articles/splatter_files/figure-html/pca-1.png
index 9669ad4fcf0ea3de8d4fbd0db97170488f9faaae..bf92e106b921a619c42b1a9a18a891ff0291ded4 100644
Binary files a/docs/articles/splatter_files/figure-html/pca-1.png and b/docs/articles/splatter_files/figure-html/pca-1.png differ
diff --git a/docs/authors.html b/docs/authors.html
index cb75a40a7d6f1b0ab3c352a5484d749064678728..a68dcbd91dcb470f657823f1bab9c8f3a062ceae 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -18,13 +18,24 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="pkgdown.css" rel="stylesheet">
-<script src="jquery.sticky-kit.min.js"></script>
<script src="pkgdown.js"></script>
+
+
+
<link href="extra.css" rel="stylesheet">
+<meta property="og:title" content="Citation and Authors" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +45,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +68,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +83,13 @@
</a>
</li>
<li>
- <a href="articles/splatter.html">Get Started</a>
+ <a href="articles/splatter.html">Get started</a>
</li>
<li>
<a href="reference/index.html">Reference</a>
</li>
<li>
- <a href="news/index.html">News</a>
+ <a href="news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +101,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,9 +109,8 @@
</header>
- <div class="row">
+<div class="row">
<div class="contents col-md-9">
-
<div class="page-header">
<h1>Citation</h1>
</div>
@@ -121,16 +134,16 @@ doi: <a href="http://doi.org/10.1186/s13059-017-1305-0">10.1186/s13059-017-1305-
<ul class="list-unstyled">
<li>
- <p><strong>Luke Zappia</strong>. Author, maintainer.
- <br /><small>0000-0001-7744-8565</small></p>
+ <p><strong>Luke Zappia</strong>. Author, maintainer. <a href='https://orcid.org/0000-0001-7744-8565' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' height='16'></a>
+ </p>
</li>
<li>
- <p><strong>Belinda Phipson</strong>. Author.
- <br /><small>0000-0002-1711-7454</small></p>
+ <p><strong>Belinda Phipson</strong>. Author. <a href='https://orcid.org/0000-0002-1711-7454' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' height='16'></a>
+ </p>
</li>
<li>
- <p><strong>Alicia Oshlack</strong>. Author.
- <br /><small>0000-0001-9788-5690</small></p>
+ <p><strong>Alicia Oshlack</strong>. Author. <a href='https://orcid.org/0000-0001-9788-5690' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' height='16'></a>
+ </p>
</li>
</ul>
@@ -151,5 +164,8 @@ doi: <a href="http://doi.org/10.1186/s13059-017-1305-0">10.1186/s13059-017-1305-
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/docsearch.css b/docs/docsearch.css
new file mode 100644
index 0000000000000000000000000000000000000000..e5f1fe1dfa2c34c51fe941829b511acd8c763301
--- /dev/null
+++ b/docs/docsearch.css
@@ -0,0 +1,148 @@
+/* Docsearch -------------------------------------------------------------- */
+/*
+ Source: https://github.com/algolia/docsearch/
+ License: MIT
+*/
+
+.algolia-autocomplete {
+ display: block;
+ -webkit-box-flex: 1;
+ -ms-flex: 1;
+ flex: 1
+}
+
+.algolia-autocomplete .ds-dropdown-menu {
+ width: 100%;
+ min-width: none;
+ max-width: none;
+ padding: .75rem 0;
+ background-color: #fff;
+ background-clip: padding-box;
+ border: 1px solid rgba(0, 0, 0, .1);
+ box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+}
+
+@media (min-width:768px) {
+ .algolia-autocomplete .ds-dropdown-menu {
+ width: 175%
+ }
+}
+
+.algolia-autocomplete .ds-dropdown-menu::before {
+ display: none
+}
+
+.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+ padding: 0;
+ background-color: rgb(255,255,255);
+ border: 0;
+ max-height: 80vh;
+}
+
+.algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
+ margin-top: 0
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion {
+ padding: 0;
+ overflow: visible
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--category-header {
+ padding: .125rem 1rem;
+ margin-top: 0;
+ font-size: 1.3em;
+ font-weight: 500;
+ color: #00008B;
+ border-bottom: 0
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
+ float: none;
+ padding-top: 0
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
+ float: none;
+ width: auto;
+ padding: 0;
+ text-align: left
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--content {
+ float: none;
+ width: auto;
+ padding: 0
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--content::before {
+ display: none
+}
+
+.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
+ padding-top: .75rem;
+ margin-top: .75rem;
+ border-top: 1px solid rgba(0, 0, 0, .1)
+}
+
+.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+ display: block;
+ padding: .1rem 1rem;
+ margin-bottom: 0.1;
+ font-size: 1.0em;
+ font-weight: 400
+ /* display: none */
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--title {
+ display: block;
+ padding: .25rem 1rem;
+ margin-bottom: 0;
+ font-size: 0.9em;
+ font-weight: 400
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--text {
+ padding: 0 1rem .5rem;
+ margin-top: -.25rem;
+ font-size: 0.8em;
+ font-weight: 400;
+ line-height: 1.25
+}
+
+.algolia-autocomplete .algolia-docsearch-footer {
+ width: 110px;
+ height: 20px;
+ z-index: 3;
+ margin-top: 10.66667px;
+ float: right;
+ font-size: 0;
+ line-height: 0;
+}
+
+.algolia-autocomplete .algolia-docsearch-footer--logo {
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+ background-repeat: no-repeat;
+ background-position: 50%;
+ background-size: 100%;
+ overflow: hidden;
+ text-indent: -9000px;
+ width: 100%;
+ height: 100%;
+ display: block;
+ transform: translate(-8px);
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--highlight {
+ color: #FF8C00;
+ background: rgba(232, 189, 54, 0.1)
+}
+
+
+.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
+ box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+}
+
+.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
+ background-color: rgba(192, 192, 192, .15)
+}
diff --git a/docs/docsearch.js b/docs/docsearch.js
new file mode 100644
index 0000000000000000000000000000000000000000..b35504cd3a282816130a16881f3ebeead9c1bcb4
--- /dev/null
+++ b/docs/docsearch.js
@@ -0,0 +1,85 @@
+$(function() {
+
+ // register a handler to move the focus to the search bar
+ // upon pressing shift + "/" (i.e. "?")
+ $(document).on('keydown', function(e) {
+ if (e.shiftKey && e.keyCode == 191) {
+ e.preventDefault();
+ $("#search-input").focus();
+ }
+ });
+
+ $(document).ready(function() {
+ // do keyword highlighting
+ /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
+ var mark = function() {
+
+ var referrer = document.URL ;
+ var paramKey = "q" ;
+
+ if (referrer.indexOf("?") !== -1) {
+ var qs = referrer.substr(referrer.indexOf('?') + 1);
+ var qs_noanchor = qs.split('#')[0];
+ var qsa = qs_noanchor.split('&');
+ var keyword = "";
+
+ for (var i = 0; i < qsa.length; i++) {
+ var currentParam = qsa[i].split('=');
+
+ if (currentParam.length !== 2) {
+ continue;
+ }
+
+ if (currentParam[0] == paramKey) {
+ keyword = decodeURIComponent(currentParam[1].replace(/\+/g, "%20"));
+ }
+ }
+
+ if (keyword !== "") {
+ $(".contents").unmark({
+ done: function() {
+ $(".contents").mark(keyword);
+ }
+ });
+ }
+ }
+ };
+
+ mark();
+ });
+});
+
+/* Search term highlighting ------------------------------*/
+
+function matchedWords(hit) {
+ var words = [];
+
+ var hierarchy = hit._highlightResult.hierarchy;
+ // loop to fetch from lvl0, lvl1, etc.
+ for (var idx in hierarchy) {
+ words = words.concat(hierarchy[idx].matchedWords);
+ }
+
+ var content = hit._highlightResult.content;
+ if (content) {
+ words = words.concat(content.matchedWords);
+ }
+
+ // return unique words
+ var words_uniq = [...new Set(words)];
+ return words_uniq;
+}
+
+function updateHitURL(hit) {
+
+ var words = matchedWords(hit);
+ var url = "";
+
+ if (hit.anchor) {
+ url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+ } else {
+ url = hit.url + '?q=' + escape(words.join(" "));
+ }
+
+ return url;
+}
diff --git a/docs/index.html b/docs/index.html
index b6a03e64a033969e786de401159d245230cf272a..d9fecf4a9ef3948c843b7f170aac62de6255b4cf 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -8,20 +8,24 @@
<title>Simple Simulation of Single-cell RNA Sequencing Data • Splatter</title>
<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="jquery.sticky-kit.min.js"></script><script src="pkgdown.js"></script><link href="extra.css" rel="stylesheet">
+<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
+<script src="pkgdown.js"></script><link href="extra.css" rel="stylesheet">
+<meta property="og:title" content="Simple Simulation of Single-cell RNA Sequencing Data">
+<meta property="og:description" content="Splatter is a package for the simulation of single-cell RNA
+ sequencing count data. It provides a simple interface for creating complex
+ simulations that are reproducible and well-documented. Parameters can be
+ estimated from real data and functions are provided for comparing real and
+ simulated datasets.">
+<meta name="twitter:card" content="summary">
<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Google analytics --><script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script><script>
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
<body>
@@ -34,8 +38,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -45,13 +53,13 @@
</a>
</li>
<li>
- <a href="articles/splatter.html">Get Started</a>
+ <a href="articles/splatter.html">Get started</a>
</li>
<li>
<a href="reference/index.html">Reference</a>
</li>
<li>
- <a href="news/index.html">News</a>
+ <a href="news/index.html">Changelog</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
@@ -84,26 +92,29 @@
</ul>
<p>Splatter is built on top of <a href="https://github.com/davismcc/scater"><code>scater</code></a> and stores simulations in <a href="https://github.com/drisso/SingleCellExperiment"><code>SingleCellExperiment</code></a> objects. Splatter also has functions for comparing simulations and real datasets.</p>
<p><strong>!Please note!</strong> This site provides documentation for the development version of Splatter. For details on the current release please refer to <a href="https://bioconductor.org/packages/splatter" class="uri">https://bioconductor.org/packages/splatter</a>.</p>
-<div class="section level2">
-<h2>Installation.</h2>
-<div class="section level3">
-<h3>Release version</h3>
+<div id="installation-" class="section level2">
+<h2 class="hasAnchor">
+<a href="#installation-" class="anchor"></a>Installation.</h2>
+<div id="release-version" class="section level3">
+<h3 class="hasAnchor">
+<a href="#release-version" class="anchor"></a>Release version</h3>
<p>Splatter has been accepted into the latest version of <a href="https://bioconductor.org/packages/splatter">Bioconductor</a> and hence requires the latest version of R (>=3.4).</p>
-<p>If you have these installed Splatter can be installed from Bioconductor using <code>biocLite</code>:</p>
-<pre class="{r}"><code>source("https://bioconductor.org/biocLite.R")
-biocLite("splatter")</code></pre>
+<p>It can be installed from Bioconductor with:</p>
+<pre class="{r}"><code>if (!requireNamespace("BiocManager", quietly=TRUE))
+ install.packages("BiocManager")
+BiocManager::install("splatter")</code></pre>
<p>If you wish to build a local version of the vignette use:</p>
-<pre class="{r}"><code><a href="http://www.rdocumentation.org/packages/BiocInstaller/topics/biocLite">biocLite("splatter", build_vignettes=TRUE)</a></code></pre>
+<pre class="{r}"><code><a href="http://www.rdocumentation.org/packages/BiocManager/topics/install">BiocManager::install("splatter", build_vignettes=TRUE)</a></code></pre>
<p>This will also build the vignette and install all suggested dependencies (which aren’t required for core functionality). Building the vignette may sometimes fail when run from the command line, if this happens try running the install command in RStudio.</p>
</div>
-<div class="section level3">
-<h3>Development version</h3>
+<div id="development-version" class="section level3">
+<h3 class="hasAnchor">
+<a href="#development-version" class="anchor"></a>Development version</h3>
<p>If you want to try the <a href="https://bioconductor.org/packages/devel/bioc/html/splatter.html">development version</a> this can also be installed from Bioconductor:</p>
-<pre class="{r}"><code>library(BiocInstaller)
-useDevel()
-biocValid() # checks for out of date packages
-biocLite() # (optional) updates out of date packages
-biocLite("splatter")</code></pre>
+<pre class="{r}"><code>library(BiocManager)
+valid() # checks for out of date packages
+BiocManager::install() # (optional) updates out of date packages
+BiocManager::install("splatter")</code></pre>
<p>Depending on the current release cycle you may also need to install the development version of R. See <a href="https://www.bioconductor.org/developers/how-to/useDevel/">here</a> for more details.</p>
<p>Alternatively the development version can be installed directly from <a href="https://github.com/Oshlack/splatter">Github</a>:</p>
<pre class="{r}"><code><a href="http://www.rdocumentation.org/packages/devtools/topics/install">devtools::install("Oshlack/splatter")</a></code></pre>
@@ -113,7 +124,8 @@ biocLite("splatter")</code></pre>
</div>
<div class="col-md-3" id="sidebar">
- <h2>Links</h2>
+ <div class="links">
+<h2>Links</h2>
<ul class="list-unstyled">
<li>Download from BIOC at <br><a href="https://www.bioconductor.org/packages/splatter">https://​www.bioconductor.org/​packages/​splatter</a>
</li>
@@ -122,21 +134,31 @@ biocLite("splatter")</code></pre>
<li>Report a bug at <br><a href="https://github.com/Oshlack/splatter/issues">https://​github.com/​Oshlack/​splatter/​issues</a>
</li>
</ul>
+</div>
+<div class="license">
<h2>License</h2>
-<p><a href="https://www.r-project.org/Licenses/GPL-3">GPL-3</a> + file <a href="LICENSE.html">LICENSE</a></p>
+<ul class="list-unstyled">
+<li>
+<a href="https://www.r-project.org/Licenses/GPL-3">GPL-3</a> + file <a href="LICENSE-text.html">LICENSE</a>
+</li>
+</ul>
+</div>
+<div class="citation">
<h2>Citation</h2>
<ul class="list-unstyled">
<li><a href="authors.html">Citing splatter</a></li>
</ul>
+</div>
+<div class="developers">
<h2>Developers</h2>
<ul class="list-unstyled">
-<li>Luke Zappia <br><small class="roles"> Author, maintainer </small> <br><small>(0000-0001-7744-8565)</small>
-</li>
-<li>Belinda Phipson <br><small class="roles"> Author </small> <br><small>(0000-0002-1711-7454)</small>
-</li>
-<li>Alicia Oshlack <br><small class="roles"> Author </small> <br><small>(0000-0001-9788-5690)</small>
-</li>
+<li>Luke Zappia <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0001-7744-8565" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" height="16"></a> </li>
+<li>Belinda Phipson <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0002-1711-7454" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" height="16"></a> </li>
+<li>Alicia Oshlack <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0001-9788-5690" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" height="16"></a> </li>
</ul>
+</div>
+
+ <div class="dev-status">
<h2>Dev status</h2>
<ul class="list-unstyled">
<li><a href="https://travis-ci.org/Oshlack/splatter"><img src="https://travis-ci.org/Oshlack/splatter.svg?branch=master" alt="Travis-CI Build Status"></a></li>
@@ -147,6 +169,7 @@ biocLite("splatter")</code></pre>
<li><a href="https://bioconductor.org/packages/devel/bioc/html/splatter.html"><img src="https://bioconductor.org/shields/downloads/splatter.svg" alt="Bioconductor Downloads"></a></li>
</ul>
</div>
+</div>
</div>
@@ -161,5 +184,7 @@ biocLite("splatter")</code></pre>
</footer>
</div>
+
+
</body>
</html>
diff --git a/docs/news/index.html b/docs/news/index.html
index ea9dd90ffad66fee5a93c55f064295b6ddc9902c..711ca5fe7e5f3513da3b67bb68bb4bafcee3af9e 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>All news • Splatter</title>
+<title>Changelog • Splatter</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -18,13 +18,24 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Changelog" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +45,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +68,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +83,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +101,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,33 +109,125 @@
</header>
- <div class="row">
-
- <div class="col-md-9">
+<div class="row">
+ <div class="col-md-9 contents">
<div class="page-header">
- <h1>Change log <small>All releases</small></h1>
+ <h1>Changelog <small></small></h1>
+ <small>Source: <a href='https://github.com/Oshlack/splatter/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
- <div class="contents">
- <div class="section level2">
-<h2>Version 1.5.0 (2018-01-02)</h2>
+ <div id="version-1-7-0-2018-11-01" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-7-0-2018-11-01" class="anchor"></a>Version 1.7.0 (2018-11-01)</h2>
+<p>Bioconductor 3.9 devel</p>
+</div>
+ <div id="version-1-6-0-2018-11-01" class="section level1">
+<h1 class="page-header">
+<a href="#version-1-6-0-2018-11-01" class="anchor"></a>Version 1.6.0 (2018-11-01)</h1>
+<p>Bioconductor 3.8 release</p>
+<div id="version-1-5-8-2018-10-22" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-5-8-2018-10-22" class="anchor"></a>Version 1.5.8 (2018-10-22)</h2>
+<ul>
+<li>Add WithSpikes argument when calling BASiCS::BASiCS_MCMC()</li>
+</ul>
+</div>
+<div id="version-1-5-7-2018-10-03" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-5-7-2018-10-03" class="anchor"></a>Version 1.5.7 (2018-10-03)</h2>
+<ul>
+<li>Fix BASiCSEstimate tests</li>
+</ul>
+</div>
+<div id="version-1-5-4-2018-08-30" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-5-4-2018-08-30" class="anchor"></a>Version 1.5.4 (2018-08-30)</h2>
+<ul>
+<li>Fix installation instructions</li>
+</ul>
+</div>
+<div id="version-1-5-3-2018-08-20" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-5-3-2018-08-20" class="anchor"></a>Version 1.5.3 (2018-08-20)</h2>
+<ul>
+<li>Fix bug in BASiCSEstimate when no spike-ins provided</li>
+</ul>
+<div id="version-1-5-2-9000-2018-08-16" class="section level3">
+<h3 class="hasAnchor">
+<a href="#version-1-5-2-9000-2018-08-16" class="anchor"></a>Version 1.5.2.9000 (2018-08-16)</h3>
+<ul>
+<li>Add missing regression argument to BASiCSEstimate</li>
+<li>Add new BASiCS tests</li>
+</ul>
+</div>
+</div>
+<div id="version-1-5-2-2018-08-16" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-5-2-2018-08-16" class="anchor"></a>Version 1.5.2 (2018-08-16)</h2>
+<ul>
+<li>Fix bug in getLNormFactors when reversing factors less than one</li>
+<li>Update documentation to new Roxygen version (6.1.0)</li>
+<li>Change varible name in vignette for compatibility with scater</li>
+<li>Add suggested package checks to tests</li>
+</ul>
+</div>
+<div id="version-1-5-1-2018-06-12" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-5-1-2018-06-12" class="anchor"></a>Version 1.5.1 (2018-06-12)</h2>
+<ul>
+<li>Fix normality testing error in splatEstLib</li>
+<li>Correct p-value cutoff in normality test</li>
+<li>Sample library sizes for normality testing if > 5000 cells</li>
+</ul>
+</div>
+<div id="version-1-5-0-2018-05-02" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-5-0-2018-05-02" class="anchor"></a>Version 1.5.0 (2018-05-02)</h2>
<ul>
<li>Bioconductor 3.7 devel</li>
</ul>
</div>
- <div class="section level1">
-<h1>Version 1.4.0 (2018-01-02)</h1>
+<div id="version-1-4-3-2018-08-20" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-4-3-2018-08-20" class="anchor"></a>Version 1.4.3 (2018-08-20)</h2>
+<ul>
+<li>Fix bug in BASiCSEstimate when no spike-ins provided</li>
+</ul>
+</div>
+<div id="version-1-4-2-2018-08-16" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-4-2-2018-08-16" class="anchor"></a>Version 1.4.2 (2018-08-16)</h2>
+<ul>
+<li>Add missing regression argument to BASiCSEstimate</li>
+<li>Add new BASiCS tests</li>
+</ul>
+</div>
+<div id="version-1-4-1-2018-06-12" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-4-1-2018-06-12" class="anchor"></a>Version 1.4.1 (2018-06-12)</h2>
+<ul>
+<li>Fix normality testing error in splatEstLib</li>
+<li>Correct p-value cutoff in normality test</li>
+<li>Sample library sizes for normality testing if > 5000 cells</li>
+</ul>
+</div>
+</div>
+ <div id="version-1-4-0-2018-05-02" class="section level1">
+<h1 class="page-header">
+<a href="#version-1-4-0-2018-05-02" class="anchor"></a>Version 1.4.0 (2018-05-02)</h1>
<ul>
<li>Bioconductor 3.7 release</li>
</ul>
-<div class="section level2">
-<h2>Version 1.3.6 (2018-04-30)</h2>
+<div id="version-1-3-6-2018-04-30" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-3-6-2018-04-30" class="anchor"></a>Version 1.3.6 (2018-04-30)</h2>
<ul>
<li>Set seed in sparseDCEstimate tests</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 1.3.5 (2018-04-25)</h2>
+<div id="version-1-3-5-2018-04-25" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-3-5-2018-04-25" class="anchor"></a>Version 1.3.5 (2018-04-25)</h2>
<ul>
<li>Replace dropout.present with dropout.type in SplatParams
<ul>
@@ -130,8 +236,9 @@
</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 1.3.4 (2018-04-19)</h2>
+<div id="version-1-3-4-2018-04-19" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-3-4-2018-04-19" class="anchor"></a>Version 1.3.4 (2018-04-19)</h2>
<ul>
<li>Add option to use a normal distribution for library sizes in Splat simulations</li>
<li>Add SparseDC simulation</li>
@@ -142,14 +249,16 @@
<li>Improve warning message when fitting means in splatEstimate fails</li>
<li>Simplify problematic documentation links</li>
</ul>
-<div class="section level3">
-<h3>Version 1.3.3.9010 (2018-04-12)</h3>
+<div id="version-1-3-3-9010-2018-04-12" class="section level3">
+<h3 class="hasAnchor">
+<a href="#version-1-3-3-9010-2018-04-12" class="anchor"></a>Version 1.3.3.9010 (2018-04-12)</h3>
<ul>
<li>Add option to use a normal distribution for library sizes in Splat simulations</li>
</ul>
</div>
-<div class="section level3">
-<h3>Version 1.3.3.9000 (2018-04-12)</h3>
+<div id="version-1-3-3-9000-2018-04-12" class="section level3">
+<h3 class="hasAnchor">
+<a href="#version-1-3-3-9000-2018-04-12" class="anchor"></a>Version 1.3.3.9000 (2018-04-12)</h3>
<ul>
<li>Replace dropout.present with dropout.type in SplatParams
<ul>
@@ -159,14 +268,16 @@
</ul>
</div>
</div>
-<div class="section level2">
-<h2>Version 1.3.3 (2018-03-27)</h2>
+<div id="version-1-3-3-2018-03-27" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-3-3-2018-03-27" class="anchor"></a>Version 1.3.3 (2018-03-27)</h2>
<ul>
<li>Fix parameter passing bug in scDDEstimate</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 1.3.2 (2018-01-31)</h2>
+<div id="version-1-3-2-2018-01-31" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-3-2-2018-01-31" class="anchor"></a>Version 1.3.2 (2018-01-31)</h2>
<ul>
<li>Fix QC names that have been changed in scater</li>
<li>Move scater to Imports and add scater version</li>
@@ -174,80 +285,92 @@
<li>Add more tests</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 1.3.1 (2018-01-03)</h2>
+<div id="version-1-3-1-2018-01-03" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-3-1-2018-01-03" class="anchor"></a>Version 1.3.1 (2018-01-03)</h2>
<ul>
<li>Fix error in vignette caused by changes in scater</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 1.3.0 (2017-10-13)</h2>
+<div id="version-1-3-0-2017-10-13" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-3-0-2017-10-13" class="anchor"></a>Version 1.3.0 (2017-10-13)</h2>
<ul>
<li>Bioconductor 3.7 devel</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 1.2.2 (2018-03-27)</h2>
+<div id="version-1-2-2-2018-03-27" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-2-2-2018-03-27" class="anchor"></a>Version 1.2.2 (2018-03-27)</h2>
<ul>
<li>Fix parameter passing bug in scDDEstimate</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 1.2.1 (2017-11-23)</h2>
+<div id="version-1-2-1-2017-11-23" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-2-1-2017-11-23" class="anchor"></a>Version 1.2.1 (2017-11-23)</h2>
<ul>
<li>Fix zinbwave installation error</li>
</ul>
</div>
</div>
- <div class="section level1">
-<h1>Version 1.2.0 (2017-10-30)</h1>
+ <div id="version-1-2-0-2017-10-30" class="section level1">
+<h1 class="page-header">
+<a href="#version-1-2-0-2017-10-30" class="anchor"></a>Version 1.2.0 (2017-10-30)</h1>
<ul>
<li>Bioconductor 3.6 release</li>
</ul>
-<div class="section level2">
-<h2>Version 1.1.8 (2017-10-13)</h2>
+<div id="version-1-1-8-2017-10-13" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-1-8-2017-10-13" class="anchor"></a>Version 1.1.8 (2017-10-13)</h2>
<ul>
<li>Add BASiCS simulation</li>
<li>Update Splatter citation</li>
<li>Update Lun2 reference</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 1.1.7 (2017-10-05)</h2>
+<div id="version-1-1-7-2017-10-05" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-1-7-2017-10-05" class="anchor"></a>Version 1.1.7 (2017-10-05)</h2>
<ul>
<li>Add PhenoPath simulation</li>
<li>Add ZINB-WaVE simulation</li>
<li>Adjust mfaSimulate output</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 1.1.6 (2017-10-02)</h2>
+<div id="version-1-1-6-2017-10-02" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-1-6-2017-10-02" class="anchor"></a>Version 1.1.6 (2017-10-02)</h2>
<ul>
<li>Update scDD version</li>
<li>Add mfa simulation</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 1.1.5 (2017-09-13)</h2>
+<div id="version-1-1-5-2017-09-13" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-1-5-2017-09-13" class="anchor"></a>Version 1.1.5 (2017-09-13)</h2>
<ul>
<li>Convert to SingleCellExperiment</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 1.1.4 (2017-08-04)</h2>
+<div id="version-1-1-4-2017-08-04" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-1-4-2017-08-04" class="anchor"></a>Version 1.1.4 (2017-08-04)</h2>
<ul>
<li>Fix group factors bug</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 1.1.3 (2017-07-20)</h2>
+<div id="version-1-1-3-2017-07-20" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-1-3-2017-07-20" class="anchor"></a>Version 1.1.3 (2017-07-20)</h2>
<ul>
<li>Add verbose option to scDDEstimate</li>
<li>Change “mean-dropout†to “mean-zeros†in compareSCESets</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 1.1.2 (2017-07-16)</h2>
+<div id="version-1-1-2-2017-07-16" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-1-2-2017-07-16" class="anchor"></a>Version 1.1.2 (2017-07-16)</h2>
<ul>
<li>Update summariseDiff</li>
<li>Update scDDEstimate, now estimates gene types</li>
@@ -255,34 +378,39 @@
<li>Import SummarizedExperiment to avoid warnings</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 1.1.1 (2017-07-07)</h2>
+<div id="version-1-1-1-2017-07-07" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-1-1-2017-07-07" class="anchor"></a>Version 1.1.1 (2017-07-07)</h2>
<ul>
<li>Add batch effects to Splat simulation</li>
<li>Make Splat group assignment probabilistic</li>
<li>Update SplatParams with new parameters</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 1.1.0 (2017-07-07)</h2>
+<div id="version-1-1-0-2017-07-07" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-1-0-2017-07-07" class="anchor"></a>Version 1.1.0 (2017-07-07)</h2>
<ul>
<li>Bioconductor 3.6 devel</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 1.0.3 (2017-05-26)</h2>
+<div id="version-1-0-3-2017-05-26" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-0-3-2017-05-26" class="anchor"></a>Version 1.0.3 (2017-05-26)</h2>
<ul>
<li>Update citation</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 1.0.2 (2017-05-15)</h2>
+<div id="version-1-0-2-2017-05-15" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-0-2-2017-05-15" class="anchor"></a>Version 1.0.2 (2017-05-15)</h2>
<ul>
<li>Fix error handling when fitting means</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 1.0.1 (2017-04-28)</h2>
+<div id="version-1-0-1-2017-04-28" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-0-1-2017-04-28" class="anchor"></a>Version 1.0.1 (2017-04-28)</h2>
<ul>
<li>Fix scales in some difference plots</li>
<li>Fix colours in difference plots</li>
@@ -290,13 +418,15 @@
</ul>
</div>
</div>
- <div class="section level1">
-<h1>Version 1.0.0 (2017-04-28)</h1>
+ <div id="version-1-0-0-2017-04-28" class="section level1">
+<h1 class="page-header">
+<a href="#version-1-0-0-2017-04-28" class="anchor"></a>Version 1.0.0 (2017-04-28)</h1>
<ul>
<li>Bioconductor 3.5 release</li>
</ul>
-<div class="section level2">
-<h2>Version 0.99.15 (2017-04-14)</h2>
+<div id="version-0-99-15-2017-04-14" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-99-15-2017-04-14" class="anchor"></a>Version 0.99.15 (2017-04-14)</h2>
<ul>
<li>Add summariseDiff function</li>
<li>Add BPPARAM argument to scDDSimulate</li>
@@ -305,24 +435,27 @@
<li>Remove estimation of dropout.present</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 0.99.14 (2017-03-28)</h2>
+<div id="version-0-99-14-2017-03-28" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-99-14-2017-03-28" class="anchor"></a>Version 0.99.14 (2017-03-28)</h2>
<ul>
<li>Add functions for making comparison panels</li>
<li>Add panel section to vignette</li>
<li>Change variance plot scale (for consistency)</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 0.99.13 (2017-03-25)</h2>
+<div id="version-0-99-13-2017-03-25" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-99-13-2017-03-25" class="anchor"></a>Version 0.99.13 (2017-03-25)</h2>
<ul>
<li>Modify how Lun2Params stores gene paramters to use data.frame</li>
<li>Move sampling of genes/cells to lun2Simulate</li>
<li>Return to old Lun2 nGenes estimate</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 0.99.12 (2017-03-22)</h2>
+<div id="version-0-99-12-2017-03-22" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-99-12-2017-03-22" class="anchor"></a>Version 0.99.12 (2017-03-22)</h2>
<ul>
<li>Add diffSCESets function</li>
<li>Update compareSCESets plots</li>
@@ -331,8 +464,9 @@
<li>Add infinte bcv.df warning to splatSimulate</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 0.99.11 (2017-03-20)</h2>
+<div id="version-0-99-11-2017-03-20" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-99-11-2017-03-20" class="anchor"></a>Version 0.99.11 (2017-03-20)</h2>
<ul>
<li>Add parallel option to lun2Estimate</li>
<li>Allow non-integer library sizes in Lun2Params</li>
@@ -340,8 +474,9 @@
<li>Adjust comparison plots</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 0.99.10 (2017-03-07)</h2>
+<div id="version-0-99-10-2017-03-07" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-99-10-2017-03-07" class="anchor"></a>Version 0.99.10 (2017-03-07)</h2>
<ul>
<li>Improve Splat estimation procedure</li>
<li>Update default Splat parameters</li>
@@ -349,80 +484,92 @@
<li>Add MeanZeros plot to compareSCESets</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 0.99.9 (2017-02-02)</h2>
+<div id="version-0-99-9-2017-02-02" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-99-9-2017-02-02" class="anchor"></a>Version 0.99.9 (2017-02-02)</h2>
<ul>
<li>Add addGeneLengths function</li>
<li>Update scDD reference</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 0.99.8 (2017-01-23)</h2>
+<div id="version-0-99-8-2017-01-23" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-99-8-2017-01-23" class="anchor"></a>Version 0.99.8 (2017-01-23)</h2>
<ul>
<li>Fix bug that meant non-linear path factors weren’t stored in output</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 0.99.7 (2017-01-10)</h2>
+<div id="version-0-99-7-2017-01-10" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-99-7-2017-01-10" class="anchor"></a>Version 0.99.7 (2017-01-10)</h2>
<ul>
<li>Small changes to avoid NOTEs and reduce check time</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 0.99.6 (2016-12-29)</h2>
+<div id="version-0-99-6-2016-12-29" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-99-6-2016-12-29" class="anchor"></a>Version 0.99.6 (2016-12-29)</h2>
<ul>
<li>Add installation to vignette</li>
<li>Add detail about counts matrix to vignette</li>
<li>Replace 1:x with seq_len/seq_along</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 0.99.5 (2016-12-28)</h2>
+<div id="version-0-99-5-2016-12-28" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-99-5-2016-12-28" class="anchor"></a>Version 0.99.5 (2016-12-28)</h2>
<ul>
<li>Set R_TESTS environment</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 0.99.4 (2016-12-23)</h2>
+<div id="version-0-99-4-2016-12-23" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-99-4-2016-12-23" class="anchor"></a>Version 0.99.4 (2016-12-23)</h2>
<ul>
<li>Version bump to start build</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 0.99.3 (2016-12-21)</h2>
+<div id="version-0-99-3-2016-12-21" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-99-3-2016-12-21" class="anchor"></a>Version 0.99.3 (2016-12-21)</h2>
<ul>
<li>Fix to match Bioconductor version of scDD</li>
<li>Add logo to repository</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 0.99.2 (2016-12-13)</h2>
+<div id="version-0-99-2-2016-12-13" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-99-2-2016-12-13" class="anchor"></a>Version 0.99.2 (2016-12-13)</h2>
<ul>
<li>Add rownames, colnames to matrices in splatSimulate, lunSimulate</li>
<li>Bump R version to 3.4</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 0.99.1 (2016-12-12)</h2>
+<div id="version-0-99-1-2016-12-12" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-99-1-2016-12-12" class="anchor"></a>Version 0.99.1 (2016-12-12)</h2>
<ul>
<li>Address Biocondutor build warnings, notes</li>
</ul>
</div>
</div>
- <div class="section level1">
-<h1>Version 0.99.0 (2016-12-05)</h1>
+ <div id="version-0-99-0-2016-12-05" class="section level1">
+<h1 class="page-header">
+<a href="#version-0-99-0-2016-12-05" class="anchor"></a>Version 0.99.0 (2016-12-05)</h1>
<ul>
<li>Submit to Bioconductor</li>
</ul>
-<div class="section level2">
-<h2>Version 0.12.1 (2016-11-25)</h2>
+<div id="version-0-12-1-2016-11-25" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-12-1-2016-11-25" class="anchor"></a>Version 0.12.1 (2016-11-25)</h2>
<ul>
<li>Fix bug in compareSCESets</li>
<li>Dataset order is now kept in plots</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 0.12.0 (2016-10-25)</h2>
+<div id="version-0-12-0-2016-10-25" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-12-0-2016-10-25" class="anchor"></a>Version 0.12.0 (2016-10-25)</h2>
<ul>
<li>Add compareSCESets function</li>
<li>Update vignette</li>
@@ -430,97 +577,109 @@
<li>Add logo</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 0.11.1 (2016-11-23)</h2>
+<div id="version-0-11-1-2016-11-23" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-11-1-2016-11-23" class="anchor"></a>Version 0.11.1 (2016-11-23)</h2>
<ul>
<li>Fix bug in splatSimulatePaths that caused NAs</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 0.11.0 (2016-11-22)</h2>
+<div id="version-0-11-0-2016-11-22" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-11-0-2016-11-22" class="anchor"></a>Version 0.11.0 (2016-11-22)</h2>
<ul>
<li>Make compatible with Bioconductor 3.4</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 0.10.1 (2016-10-17)</h2>
+<div id="version-0-10-1-2016-10-17" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-10-1-2016-10-17" class="anchor"></a>Version 0.10.1 (2016-10-17)</h2>
<ul>
<li>Fix error for SCESets in lun2Estimate, scDDEstimate</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 0.10.0 (2016-10-16)</h2>
+<div id="version-0-10-0-2016-10-16" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-10-0-2016-10-16" class="anchor"></a>Version 0.10.0 (2016-10-16)</h2>
<ul>
<li>Add listSims function</li>
<li>Add vignette</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 0.9.0 (2016-10-15)</h2>
+<div id="version-0-9-0-2016-10-15" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-9-0-2016-10-15" class="anchor"></a>Version 0.9.0 (2016-10-15)</h2>
<ul>
<li>Add scDD simulation</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 0.8.0 (2016-10-15)</h2>
+<div id="version-0-8-0-2016-10-15" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-8-0-2016-10-15" class="anchor"></a>Version 0.8.0 (2016-10-15)</h2>
<ul>
<li>Add Lun2 simulation</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 0.7.0 (2016-10-14)</h2>
+<div id="version-0-7-0-2016-10-14" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-7-0-2016-10-14" class="anchor"></a>Version 0.7.0 (2016-10-14)</h2>
<ul>
<li>Redesign how parameters are stored</li>
<li>Each simulation now has it’s own S4 Params class</li>
<li>Modify exisiting simulations to use new parameter objects</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 0.6.0 (2016-10-12)</h2>
+<div id="version-0-6-0-2016-10-12" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-6-0-2016-10-12" class="anchor"></a>Version 0.6.0 (2016-10-12)</h2>
<ul>
<li>Add Lun simulation</li>
<li>Modify splatParams to take Lun parameters</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 0.5.0 (2016-10-12)</h2>
+<div id="version-0-5-0-2016-10-12" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-5-0-2016-10-12" class="anchor"></a>Version 0.5.0 (2016-10-12)</h2>
<ul>
<li>Add simple simulation</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 0.4.0 (2016-10-12)</h2>
+<div id="version-0-4-0-2016-10-12" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-4-0-2016-10-12" class="anchor"></a>Version 0.4.0 (2016-10-12)</h2>
<ul>
<li>Add splatter simulations</li>
<li>Modify some parts of splatParams and fix bugs</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 0.3.0 (2016-10-06)</h2>
+<div id="version-0-3-0-2016-10-06" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-3-0-2016-10-06" class="anchor"></a>Version 0.3.0 (2016-10-06)</h2>
<ul>
<li>Added parameter estimation functions</li>
</ul>
</div>
-<div class="section level2">
-<h2>Version 0.2.0 (2016-10-06)</h2>
+<div id="version-0-2-0-2016-10-06" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-2-0-2016-10-06" class="anchor"></a>Version 0.2.0 (2016-10-06)</h2>
<ul>
<li>Added splatParams object</li>
<li>Added functions for interacting with splatParams</li>
</ul>
</div>
</div>
- </div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
- <li><a href="#NA">1.5.0</a></li>
- <li><a href="#NA">1.4.0</a></li>
- <li><a href="#NA">1.2.0</a></li>
- <li><a href="#NA">1.0.0</a></li>
- <li><a href="#NA">0.99.0</a></li>
+ <li><a href="#version-1-7-0-2018-11-01">1.7.0</a></li>
+ <li><a href="#version-1-6-0-2018-11-01">1.6.0</a></li>
+ <li><a href="#version-1-4-0-2018-05-02">1.4.0</a></li>
+ <li><a href="#version-1-2-0-2017-10-30">1.2.0</a></li>
+ <li><a href="#version-1-0-0-2017-04-28">1.0.0</a></li>
+ <li><a href="#version-0-99-0-2016-12-05">0.99.0</a></li>
</ul>
</div>
</div>
@@ -539,5 +698,8 @@
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/pkgdown.css b/docs/pkgdown.css
index 209ce57febdc449e03d16b5b0d9323cd33692873..6ca2f37ab4f657e9f79e79032b2e34e0e13397d5 100644
--- a/docs/pkgdown.css
+++ b/docs/pkgdown.css
@@ -1,13 +1,32 @@
-/* Sticker footer */
+/* Sticky footer */
+
+/**
+ * Basic idea: https://philipwalton.github.io/solved-by-flexbox/demos/sticky-footer/
+ * Details: https://github.com/philipwalton/solved-by-flexbox/blob/master/assets/css/components/site.css
+ *
+ * .Site -> body > .container
+ * .Site-content -> body > .container .row
+ * .footer -> footer
+ *
+ * Key idea seems to be to ensure that .container and __all its parents__
+ * have height set to 100%
+ *
+ */
+
+html, body {
+ height: 100%;
+}
+
body > .container {
display: flex;
- padding-top: 60px;
- min-height: calc(100vh);
+ height: 100%;
flex-direction: column;
+
+ padding-top: 60px;
}
body > .container .row {
- flex: 1;
+ flex: 1 0 auto;
}
footer {
@@ -16,6 +35,7 @@ footer {
border-top: 1px solid #e5e5e5;
color: #666;
display: flex;
+ flex-shrink: 0;
}
footer p {
margin-bottom: 0;
@@ -38,6 +58,12 @@ img {
max-width: 100%;
}
+/* Typographic tweaking ---------------------------------*/
+
+.contents h1.page-header {
+ margin-top: calc(-60px + 1em);
+}
+
/* Section anchors ---------------------------------*/
a.anchor {
@@ -68,7 +94,7 @@ a.anchor {
.contents h1, .contents h2, .contents h3, .contents h4 {
padding-top: 60px;
- margin-top: -60px;
+ margin-top: -40px;
}
/* Static header placement on mobile devices */
@@ -100,10 +126,14 @@ a.anchor {
margin-bottom: 0.5em;
}
+.orcid {
+ height: 16px;
+ vertical-align: middle;
+}
+
/* Reference index & topics ----------------------------------------------- */
.ref-index th {font-weight: normal;}
-.ref-index h2 {font-size: 20px;}
.ref-index td {vertical-align: top;}
.ref-index .alias {width: 40%;}
@@ -137,6 +167,12 @@ pre, code {
color: #333;
}
+pre code {
+ overflow: auto;
+ word-wrap: normal;
+ white-space: pre;
+}
+
pre .img {
margin: 5px 0;
}
@@ -151,6 +187,10 @@ code a, pre a {
color: #375f84;
}
+a.sourceLine:hover {
+ text-decoration: none;
+}
+
.fl {color: #1514b5;}
.fu {color: #000000;} /* function */
.ch,.st {color: #036a07;} /* string */
@@ -161,3 +201,32 @@ code a, pre a {
.error { color: orange; font-weight: bolder;}
.warning { color: #6A0366; font-weight: bolder;}
+/* Clipboard --------------------------*/
+
+.hasCopyButton {
+ position: relative;
+}
+
+.btn-copy-ex {
+ position: absolute;
+ right: 0;
+ top: 0;
+ visibility: hidden;
+}
+
+.hasCopyButton:hover button.btn-copy-ex {
+ visibility: visible;
+}
+
+/* mark.js ----------------------------*/
+
+mark {
+ background-color: rgba(255, 255, 51, 0.5);
+ border-bottom: 2px solid rgba(255, 153, 51, 0.3);
+ padding: 1px;
+}
+
+/* vertical spacing after htmlwidgets */
+.html-widget {
+ margin-bottom: 10px;
+}
diff --git a/docs/pkgdown.js b/docs/pkgdown.js
index 4b81713289040dbd19cf8e215a054f5c129a5f91..de9bd7247cf858fdc66d64631f9b67f06b170f5a 100644
--- a/docs/pkgdown.js
+++ b/docs/pkgdown.js
@@ -1,45 +1,110 @@
-$(function() {
- $("#sidebar").stick_in_parent({offset_top: 40});
- $('body').scrollspy({
- target: '#sidebar',
- offset: 60
- });
+/* http://gregfranko.com/blog/jquery-best-practices/ */
+(function($) {
+ $(function() {
+
+ $("#sidebar")
+ .stick_in_parent({offset_top: 40})
+ .on('sticky_kit:bottom', function(e) {
+ $(this).parent().css('position', 'static');
+ })
+ .on('sticky_kit:unbottom', function(e) {
+ $(this).parent().css('position', 'relative');
+ });
+
+ $('body').scrollspy({
+ target: '#sidebar',
+ offset: 60
+ });
- var cur_path = paths(location.pathname);
- $("#navbar ul li a").each(function(index, value) {
- if (value.text == "Home")
- return;
- if (value.getAttribute("href") === "#")
- return;
-
- var path = paths(value.pathname);
- if (is_prefix(cur_path, path)) {
- // Add class to parent <li>, and enclosing <li> if in dropdown
- var menu_anchor = $(value);
+ $('[data-toggle="tooltip"]').tooltip();
+
+ var cur_path = paths(location.pathname);
+ var links = $("#navbar ul li a");
+ var max_length = -1;
+ var pos = -1;
+ for (var i = 0; i < links.length; i++) {
+ if (links[i].getAttribute("href") === "#")
+ continue;
+ var path = paths(links[i].pathname);
+
+ var length = prefix_length(cur_path, path);
+ if (length > max_length) {
+ max_length = length;
+ pos = i;
+ }
+ }
+
+ // Add class to parent <li>, and enclosing <li> if in dropdown
+ if (pos >= 0) {
+ var menu_anchor = $(links[pos]);
menu_anchor.parent().addClass("active");
menu_anchor.closest("li.dropdown").addClass("active");
}
});
-});
-function paths(pathname) {
- var pieces = pathname.split("/");
- pieces.shift(); // always starts with /
+ function paths(pathname) {
+ var pieces = pathname.split("/");
+ pieces.shift(); // always starts with /
+
+ var end = pieces[pieces.length - 1];
+ if (end === "index.html" || end === "")
+ pieces.pop();
+ return(pieces);
+ }
+
+ function prefix_length(needle, haystack) {
+ if (needle.length > haystack.length)
+ return(0);
+
+ // Special case for length-0 haystack, since for loop won't run
+ if (haystack.length === 0) {
+ return(needle.length === 0 ? 1 : 0);
+ }
+
+ for (var i = 0; i < haystack.length; i++) {
+ if (needle[i] != haystack[i])
+ return(i);
+ }
- var end = pieces[pieces.length - 1];
- if (end === "index.html" || end === "")
- pieces.pop();
- return(pieces);
-}
+ return(haystack.length);
+ }
-function is_prefix(needle, haystack) {
- if (needle.length > haystack.lengh)
- return(false);
+ /* Clipboard --------------------------*/
- for (var i = 0; i < haystack.length; i++) {
- if (needle[i] != haystack[i])
- return(false);
+ function changeTooltipMessage(element, msg) {
+ var tooltipOriginalTitle=element.getAttribute('data-original-title');
+ element.setAttribute('data-original-title', msg);
+ $(element).tooltip('show');
+ element.setAttribute('data-original-title', tooltipOriginalTitle);
}
- return(true);
-}
+ if(Clipboard.isSupported()) {
+ $(document).ready(function() {
+ var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+
+ $(".examples, div.sourceCode").addClass("hasCopyButton");
+
+ // Insert copy buttons:
+ $(copyButton).prependTo(".hasCopyButton");
+
+ // Initialize tooltips:
+ $('.btn-copy-ex').tooltip({container: 'body'});
+
+ // Initialize clipboard:
+ var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+ text: function(trigger) {
+ return trigger.parentNode.textContent;
+ }
+ });
+
+ clipboardBtnCopies.on('success', function(e) {
+ changeTooltipMessage(e.trigger, 'Copied!');
+ e.clearSelection();
+ });
+
+ clipboardBtnCopies.on('error', function() {
+ changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+ });
+ });
+ }
+})(window.jQuery || window.$)
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 8da9e53a58f222c3d6af52d899915157c4726413..62c46f74eabe7b994e85a9559cb62cb7af13968e 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,6 +1,9 @@
+pandoc: 2.1.1
+pkgdown: 1.1.0
+pkgdown_sha: ~
+articles:
+ splatter: splatter.html
urls:
reference: http://oshlack.github.io/splatter/reference
article: http://oshlack.github.io/splatter/articles
-articles:
- splatter: splatter.html
diff --git a/docs/reference/BASiCSEstimate.html b/docs/reference/BASiCSEstimate.html
index 0d69930b40068e9bd51ca8465575c866ca11080b..51890b3232712fd57200b120e9e76ff119dca730 100644
--- a/docs/reference/BASiCSEstimate.html
+++ b/docs/reference/BASiCSEstimate.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Estimate BASiCS simulation parameters — BASiCSEstimate" />
+
+<meta property="og:description" content="Estimate simulation parameters for the BASiCS simulation from a real dataset." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,31 +112,37 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Estimate BASiCS simulation parameters</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/BASiCS-estimate.R'><code>R/BASiCS-estimate.R</code></a></small>
+ <div class="hidden name"><code>BASiCSEstimate.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Estimate simulation parameters for the BASiCS simulation from a real dataset.</p>
+ </div>
<pre class="usage"><span class='fu'>BASiCSEstimate</span>(<span class='no'>counts</span>, <span class='kw'>spike.info</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>batch</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>20000</span>,
- <span class='kw'>thin</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>burn</span> <span class='kw'>=</span> <span class='fl'>5000</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newBASiCSParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='kw'>progress</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
+ <span class='kw'>thin</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>burn</span> <span class='kw'>=</span> <span class='fl'>5000</span>, <span class='kw'>regression</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+ <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newBASiCSParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>progress</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
<span class='co'># S3 method for SingleCellExperiment</span>
<span class='fu'>BASiCSEstimate</span>(<span class='no'>counts</span>, <span class='kw'>spike.info</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>batch</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>20000</span>, <span class='kw'>thin</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>burn</span> <span class='kw'>=</span> <span class='fl'>5000</span>,
- <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newBASiCSParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>progress</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
+ <span class='kw'>regression</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newBASiCSParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+ <span class='kw'>progress</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
<span class='co'># S3 method for matrix</span>
-<span class='fu'>BASiCSEstimate</span>(<span class='no'>counts</span>, <span class='kw'>spike.info</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>batch</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
- <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>20000</span>, <span class='kw'>thin</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>burn</span> <span class='kw'>=</span> <span class='fl'>5000</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newBASiCSParams</a></span>(),
- <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>progress</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
+<span class='fu'>BASiCSEstimate</span>(<span class='no'>counts</span>, <span class='kw'>spike.info</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+ <span class='kw'>batch</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>20000</span>, <span class='kw'>thin</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>burn</span> <span class='kw'>=</span> <span class='fl'>5000</span>,
+ <span class='kw'>regression</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newBASiCSParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+ <span class='kw'>progress</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -151,6 +174,11 @@ a multiple of <code>thin</code>.</p></td>
<th>burn</th>
<td><p>burn-in period for the MCMC sampler. Must be in the range
<code>1 <= burn < n</code> and a multiple of <code>thin</code>.</p></td>
+ </tr>
+ <tr>
+ <th>regression</th>
+ <td><p>logical. Whether to use regression to identify
+over-dispersion. See <code><a href='http://www.rdocumentation.org/packages/BASiCS/topics/BASiCS_MCMC'>BASiCS_MCMC</a></code> for details.</p></td>
</tr>
<tr>
<th>params</th>
@@ -193,7 +221,7 @@ information is provided there must be at least two batches. See
<span class='no'>spike.info</span> <span class='kw'><-</span> <span class='fu'>data.frame</span>(<span class='kw'>Name</span> <span class='kw'>=</span> <span class='fu'>rownames</span>(<span class='no'>sc_example_counts</span>)[<span class='fl'>1</span>:<span class='fl'>10</span>],
<span class='kw'>Input</span> <span class='kw'>=</span> <span class='fu'>rnorm</span>(<span class='fl'>10</span>, <span class='fl'>500</span>, <span class='fl'>200</span>),
<span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
-<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>BASiCSEstimate</span>(<span class='no'>sc_example_counts</span>[<span class='fl'>1</span>:<span class='fl'>50</span>, <span class='fl'>1</span>:<span class='fl'>20</span>],
+<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>BASiCSEstimate</span>(<span class='no'>sc_example_counts</span>[<span class='fl'>1</span>:<span class='fl'>100</span>, <span class='fl'>1</span>:<span class='fl'>30</span>],
<span class='no'>spike.info</span>)
<span class='no'>params</span>
<span class='co'># }</span></pre>
@@ -225,5 +253,8 @@ information is provided there must be at least two batches. See
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/BASiCSParams.html b/docs/reference/BASiCSParams.html
index 721e44280c49263924766396eab2f0620eea2a7e..9c2a7b92ce80c4a7964edc3940bc085270f5ace1 100644
--- a/docs/reference/BASiCSParams.html
+++ b/docs/reference/BASiCSParams.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="The BASiCSParams class — BASiCSParams" />
+
+<meta property="og:description" content="S4 class that holds parameters for the BASiCS simulation." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,15 +112,19 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>The BASiCSParams class</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/AllClasses.R'><code>R/AllClasses.R</code></a></small>
+ <div class="hidden name"><code>BASiCSParams.Rd</code></div>
</div>
+ <div class="ref-description">
<p>S4 class that holds parameters for the BASiCS simulation.</p>
+ </div>
<h2 class="hasAnchor" id="parameters"><a class="anchor" href="#parameters"></a>Parameters</h2>
@@ -166,5 +187,8 @@
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/BASiCSSimulate.html b/docs/reference/BASiCSSimulate.html
index 34629d645e635d2f3e2da26bcd401dbf659537f6..c0992a6a4d5524a6cbbc47d6ae0c2457c3ff3cff 100644
--- a/docs/reference/BASiCSSimulate.html
+++ b/docs/reference/BASiCSSimulate.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="BASiCS simulation — BASiCSSimulate" />
+
+<meta property="og:description" content="Simulate counts using the BASiCS method." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,19 +112,23 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>BASiCS simulation</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/BASiCS-simulate.R'><code>R/BASiCS-simulate.R</code></a></small>
+ <div class="hidden name"><code>BASiCSSimulate.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Simulate counts using the BASiCS method.</p>
+ </div>
<pre class="usage"><span class='fu'>BASiCSSimulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newBASiCSParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -177,5 +198,8 @@ Single-Cell Sequencing data. PLoS Comput. Biol. (2015).</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/Lun2Params.html b/docs/reference/Lun2Params.html
index 87d793c939c22681b6237a72cefdaaa31712fb15..92ffb513141ff6c55356fa1d50dd67e06d1dc2f0 100644
--- a/docs/reference/Lun2Params.html
+++ b/docs/reference/Lun2Params.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="The Lun2Params class — Lun2Params" />
+
+<meta property="og:description" content="S4 class that holds parameters for the Lun2 simulation." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,21 +112,26 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>The Lun2Params class</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/AllClasses.R'><code>R/AllClasses.R</code></a></small>
+ <div class="hidden name"><code>Lun2Params.Rd</code></div>
</div>
+ <div class="ref-description">
<p>S4 class that holds parameters for the Lun2 simulation.</p>
+ </div>
<h2 class="hasAnchor" id="parameters"><a class="anchor" href="#parameters"></a>Parameters</h2>
- <p>The Lun2 simulation uses the following parameters:</p><dl class='dl-horizontal'>
+ <p>The Lun2 simulation uses the following parameters:</p>
+<dl class='dl-horizontal'>
<dt><code>nGenes</code></dt><dd><p>The number of genes to simulate.</p></dd>
<dt><code>nCells</code></dt><dd><p>The number of cells to simulate.</p></dd>
<dt><code>[seed]</code></dt><dd><p>Seed to use for generating random numbers.</p></dd>
@@ -172,5 +194,8 @@
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/LunParams.html b/docs/reference/LunParams.html
index c84c8c617c7f9efc18d8c89592758cd4c45e0662..67a076289bf4b4877c782ff37df868fe23e2dfa6 100644
--- a/docs/reference/LunParams.html
+++ b/docs/reference/LunParams.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="The LunParams class — LunParams" />
+
+<meta property="og:description" content="S4 class that holds parameters for the Lun simulation." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,21 +112,26 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>The LunParams class</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/AllClasses.R'><code>R/AllClasses.R</code></a></small>
+ <div class="hidden name"><code>LunParams.Rd</code></div>
</div>
+ <div class="ref-description">
<p>S4 class that holds parameters for the Lun simulation.</p>
+ </div>
<h2 class="hasAnchor" id="parameters"><a class="anchor" href="#parameters"></a>Parameters</h2>
- <p>The Lun simulation uses the following parameters:</p><dl class='dl-horizontal'>
+ <p>The Lun simulation uses the following parameters:</p>
+<dl class='dl-horizontal'>
<dt><code>nGenes</code></dt><dd><p>The number of genes to simulate.</p></dd>
<dt><code>nCells</code></dt><dd><p>The number of cells to simulate.</p></dd>
<dt><code>[nGroups]</code></dt><dd><p>The number of groups to simulate.</p></dd>
@@ -164,5 +186,8 @@
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/MFAParams.html b/docs/reference/MFAParams.html
index 5e5ac99d70c0080a3e787f3157e5310a4e57fcd8..2e5f571d4f40137f799f78a92fb688e9cd338bd4 100644
--- a/docs/reference/MFAParams.html
+++ b/docs/reference/MFAParams.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="The MFAParams class — MFAParams" />
+
+<meta property="og:description" content="S4 class that holds parameters for the mfa simulation." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,15 +112,19 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>The MFAParams class</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/AllClasses.R'><code>R/AllClasses.R</code></a></small>
+ <div class="hidden name"><code>MFAParams.Rd</code></div>
</div>
+ <div class="ref-description">
<p>S4 class that holds parameters for the mfa simulation.</p>
+ </div>
<h2 class="hasAnchor" id="parameters"><a class="anchor" href="#parameters"></a>Parameters</h2>
@@ -151,5 +172,8 @@ the mfa simulation see <code><a href='mfaSimulate.html'>mfaSimulate</a></code>.<
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/Params.html b/docs/reference/Params.html
index 6825352b634a8fa1825f59ea38b920dad90e6992..25b222320b6d26f969b59a15a863e3a25bbe29a6 100644
--- a/docs/reference/Params.html
+++ b/docs/reference/Params.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="The Params virtual class — Params" />
+
+<meta property="og:description" content="Virtual S4 class that all other Params classes inherit from." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,21 +112,26 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>The Params virtual class</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/AllClasses.R'><code>R/AllClasses.R</code></a></small>
+ <div class="hidden name"><code>Params.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Virtual S4 class that all other Params classes inherit from.</p>
+ </div>
<h2 class="hasAnchor" id="parameters"><a class="anchor" href="#parameters"></a>Parameters</h2>
- <p>The Params class defines the following parameters:</p><dl class='dl-horizontal'>
+ <p>The Params class defines the following parameters:</p>
+<dl class='dl-horizontal'>
<dt><code>nGenes</code></dt><dd><p>The number of genes to simulate.</p></dd>
<dt><code>nCells</code></dt><dd><p>The number of cells to simulate.</p></dd>
<dt><code>[seed]</code></dt><dd><p>Seed to use for generating random numbers.</p></dd>
@@ -140,5 +162,8 @@
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/PhenoParams.html b/docs/reference/PhenoParams.html
index 2c75b53dc01849419544edfc830f3f4e3e188076..449a50746511957f332d6d30dee340fd13e56690 100644
--- a/docs/reference/PhenoParams.html
+++ b/docs/reference/PhenoParams.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="The PhenoParams class — PhenoParams" />
+
+<meta property="og:description" content="S4 class that holds parameters for the PhenoPath simulation." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,21 +112,26 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>The PhenoParams class</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/AllClasses.R'><code>R/AllClasses.R</code></a></small>
+ <div class="hidden name"><code>PhenoParams.Rd</code></div>
</div>
+ <div class="ref-description">
<p>S4 class that holds parameters for the PhenoPath simulation.</p>
+ </div>
<h2 class="hasAnchor" id="parameters"><a class="anchor" href="#parameters"></a>Parameters</h2>
- <p>The PhenoPath simulation uses the following parameters:</p><dl class='dl-horizontal'>
+ <p>The PhenoPath simulation uses the following parameters:</p>
+<dl class='dl-horizontal'>
<dt><code>nGenes</code></dt><dd><p>The number of genes to simulate.</p></dd>
<dt><code>nCells</code></dt><dd><p>The number of cells to simulate.</p></dd>
<dt><code>[seed]</code></dt><dd><p>Seed to use for generating random numbers.</p></dd>
@@ -150,5 +172,8 @@ see <code><a href='phenoSimulate.html'>phenoSimulate</a></code>.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/SCDDParams.html b/docs/reference/SCDDParams.html
index c50fe4550f236ba2bbcd3e6ceef3dfd33bb1dd2e..de57312ca7a08092ec5f74a3ade2b170ae1f06e9 100644
--- a/docs/reference/SCDDParams.html
+++ b/docs/reference/SCDDParams.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="The SCDDParams class — SCDDParams" />
+
+<meta property="og:description" content="S4 class that holds parameters for the scDD simulation." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,21 +112,26 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>The SCDDParams class</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/AllClasses.R'><code>R/AllClasses.R</code></a></small>
+ <div class="hidden name"><code>SCDDParams.Rd</code></div>
</div>
+ <div class="ref-description">
<p>S4 class that holds parameters for the scDD simulation.</p>
+ </div>
<h2 class="hasAnchor" id="parameters"><a class="anchor" href="#parameters"></a>Parameters</h2>
- <p>The SCDD simulation uses the following parameters:</p><dl class='dl-horizontal'>
+ <p>The SCDD simulation uses the following parameters:</p>
+<dl class='dl-horizontal'>
<dt><code>nGenes</code></dt><dd><p>The number of genes to simulate (not used).</p></dd>
<dt><code>nCells</code></dt><dd><p>The number of cells to simulate in each condition.</p></dd>
<dt><code>[seed]</code></dt><dd><p>Seed to use for generating random numbers.</p></dd>
@@ -157,5 +179,8 @@ the scDD simulation see <code><a href='scDDSimulate.html'>scDDSimulate</a></code
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/SimpleParams.html b/docs/reference/SimpleParams.html
index 7149329bd1510066471fc3cbd40c2893e7c8b8d7..9d678e46cce9d10f580c68a3b9d8617251f37455 100644
--- a/docs/reference/SimpleParams.html
+++ b/docs/reference/SimpleParams.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="The SimpleParams class — SimpleParams" />
+
+<meta property="og:description" content="S4 class that holds parameters for the simple simulation." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,21 +112,26 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>The SimpleParams class</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/AllClasses.R'><code>R/AllClasses.R</code></a></small>
+ <div class="hidden name"><code>SimpleParams.Rd</code></div>
</div>
+ <div class="ref-description">
<p>S4 class that holds parameters for the simple simulation.</p>
+ </div>
<h2 class="hasAnchor" id="parameters"><a class="anchor" href="#parameters"></a>Parameters</h2>
- <p>The simple simulation uses the following parameters:</p><dl class='dl-horizontal'>
+ <p>The simple simulation uses the following parameters:</p>
+<dl class='dl-horizontal'>
<dt><code>nGenes</code></dt><dd><p>The number of genes to simulate.</p></dd>
<dt><code>nCells</code></dt><dd><p>The number of cells to simulate.</p></dd>
<dt><code>[seed]</code></dt><dd><p>Seed to use for generating random numbers.</p></dd>
@@ -148,5 +170,8 @@ see <code><a href='simpleSimulate.html'>simpleSimulate</a></code>.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/SparseDCParams.html b/docs/reference/SparseDCParams.html
index b106fa1fda38ead9d176e12e0109dcbb47543042..819e4e341723e17612cf0d85b20a6087d040dae0 100644
--- a/docs/reference/SparseDCParams.html
+++ b/docs/reference/SparseDCParams.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="The SparseDCParams class — SparseDCParams" />
+
+<meta property="og:description" content="S4 class that holds parameters for the SparseDC simulation." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,21 +112,26 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>The SparseDCParams class</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/AllClasses.R'><code>R/AllClasses.R</code></a></small>
+ <div class="hidden name"><code>SparseDCParams.Rd</code></div>
</div>
+ <div class="ref-description">
<p>S4 class that holds parameters for the SparseDC simulation.</p>
+ </div>
<h2 class="hasAnchor" id="parameters"><a class="anchor" href="#parameters"></a>Parameters</h2>
- <p>The SparseDC simulation uses the following parameters:</p><dl class='dl-horizontal'>
+ <p>The SparseDC simulation uses the following parameters:</p>
+<dl class='dl-horizontal'>
<dt><code>nGenes</code></dt><dd><p>The number of genes to simulate in each condition.</p></dd>
<dt><code>nCells</code></dt><dd><p>The number of cells to simulate.</p></dd>
<dt><code>[seed]</code></dt><dd><p>Seed to use for generating random numbers.</p></dd>
@@ -157,5 +179,8 @@ see <code><a href='sparseDCSimulate.html'>sparseDCSimulate</a></code>.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/SplatParams.html b/docs/reference/SplatParams.html
index 1734151e69507c1be5cf17fcc20a064dffab01ec..687e6b5670a5b2088d78c88ab1facd06accd63b8 100644
--- a/docs/reference/SplatParams.html
+++ b/docs/reference/SplatParams.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="The SplatParams class — SplatParams" />
+
+<meta property="og:description" content="S4 class that holds parameters for the Splatter simulation." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,21 +112,26 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>The SplatParams class</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/AllClasses.R'><code>R/AllClasses.R</code></a></small>
+ <div class="hidden name"><code>SplatParams.Rd</code></div>
</div>
+ <div class="ref-description">
<p>S4 class that holds parameters for the Splatter simulation.</p>
+ </div>
<h2 class="hasAnchor" id="parameters"><a class="anchor" href="#parameters"></a>Parameters</h2>
- <p>The Splatter simulation requires the following parameters:</p><dl class='dl-horizontal'>
+ <p>The Splatter simulation requires the following parameters:</p>
+<dl class='dl-horizontal'>
<dt><code>nGenes</code></dt><dd><p>The number of genes to simulate.</p></dd>
<dt><code>nCells</code></dt><dd><p>The number of cells to simulate.</p></dd>
<dt><code>[seed]</code></dt><dd><p>Seed to use for generating random numbers.</p></dd>
@@ -236,5 +258,8 @@ see <code><a href='splatSimulate.html'>splatSimulate</a></code>.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/ZINBParams.html b/docs/reference/ZINBParams.html
index b20caf51ab9229ff5810d5532db821900241acaa..9783ea87d183a03d0fa81e523017e87c3d9b1e19 100644
--- a/docs/reference/ZINBParams.html
+++ b/docs/reference/ZINBParams.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="The ZINBParams class — ZINBParams" />
+
+<meta property="og:description" content="S4 class that holds parameters for the ZINB-WaVE simulation." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,21 +112,26 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>The ZINBParams class</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/AllClasses.R'><code>R/AllClasses.R</code></a></small>
+ <div class="hidden name"><code>ZINBParams.Rd</code></div>
</div>
+ <div class="ref-description">
<p>S4 class that holds parameters for the ZINB-WaVE simulation.</p>
+ </div>
<h2 class="hasAnchor" id="parameters"><a class="anchor" href="#parameters"></a>Parameters</h2>
- <p>The ZINB-WaVE simulation uses the following parameters:</p><dl class='dl-horizontal'>
+ <p>The ZINB-WaVE simulation uses the following parameters:</p>
+<dl class='dl-horizontal'>
<dt><code>nGenes</code></dt><dd><p>The number of genes to simulate.</p></dd>
<dt><code>nCells</code></dt><dd><p>The number of cells to simulate.</p></dd>
<dt><code>[seed]</code></dt><dd><p>Seed to use for generating random numbers.</p></dd>
@@ -147,5 +169,8 @@ see <code><a href='zinbSimulate.html'>zinbSimulate</a></code>.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/addFeatureStats.html b/docs/reference/addFeatureStats.html
index 5455a8cd0d5206b9c13e9223a5805478350f1877..d60618c426830800a40af5beeee3375fc350e462 100644
--- a/docs/reference/addFeatureStats.html
+++ b/docs/reference/addFeatureStats.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Add feature statistics — addFeatureStats" />
+
+<meta property="og:description" content="Add additional feature statistics to a SingleCellExperiment object" />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,20 +112,24 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Add feature statistics</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/SCE-functions.R'><code>R/SCE-functions.R</code></a></small>
+ <div class="hidden name"><code>addFeatureStats.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Add additional feature statistics to a SingleCellExperiment object</p>
+ </div>
- <pre class="usage"><span class='fu'>addFeatureStats</span>(<span class='no'>sce</span>, <span class='kw'>value</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"counts"</span>, <span class='st'>"cpm"</span>, <span class='st'>"tpm"</span>, <span class='st'>"fpkm"</span>), <span class='kw'>log</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
- <span class='kw'>offset</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>no.zeros</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
+ <pre class="usage"><span class='fu'>addFeatureStats</span>(<span class='no'>sce</span>, <span class='kw'>value</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"counts"</span>, <span class='st'>"cpm"</span>, <span class='st'>"tpm"</span>, <span class='st'>"fpkm"</span>),
+ <span class='kw'>log</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>offset</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>no.zeros</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -176,5 +197,8 @@ analysis packages.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/addGeneLengths.html b/docs/reference/addGeneLengths.html
index 592a18620c3a1d616b803e73d539c92ff4613512..8e234151c5347cabc79e4a5bb966c1fae7006836 100644
--- a/docs/reference/addGeneLengths.html
+++ b/docs/reference/addGeneLengths.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Add gene lengths — addGeneLengths" />
+
+<meta property="og:description" content="Add gene lengths to an SingleCellExperiment object" />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,20 +112,24 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Add gene lengths</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/SCE-functions.R'><code>R/SCE-functions.R</code></a></small>
+ <div class="hidden name"><code>addGeneLengths.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Add gene lengths to an SingleCellExperiment object</p>
+ </div>
<pre class="usage"><span class='fu'>addGeneLengths</span>(<span class='no'>sce</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"generate"</span>, <span class='st'>"sample"</span>), <span class='kw'>loc</span> <span class='kw'>=</span> <span class='fl'>7.9</span>,
<span class='kw'>scale</span> <span class='kw'>=</span> <span class='fl'>0.7</span>, <span class='kw'>lengths</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -154,14 +175,14 @@ vector.</p>
<pre class="examples"><div class='input'><span class='co'># Default generate method</span>
<span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>()</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'>addGeneLengths</span>(<span class='no'>sce</span>)
<span class='fu'>head</span>(<span class='fu'>rowData</span>(<span class='no'>sce</span>))</div><div class='output co'>#> DataFrame with 6 rows and 3 columns
-#> Gene GeneMean Length
-#> <factor> <numeric> <numeric>
-#> 1 Gene1 1.08758043949668 1146
-#> 2 Gene2 0.0748348805693826 2984
-#> 3 Gene3 4.39134549612356e-05 4834
-#> 4 Gene4 2.50529281404367 2495
-#> 5 Gene5 6.13362394694411 3769
-#> 6 Gene6 1.42330674557448 4022</div><div class='input'># Sample method (human coding genes)
+#> Gene GeneMean Length
+#> <factor> <numeric> <numeric>
+#> 1 Gene1 0.197443857880758 1235
+#> 2 Gene2 5.46465220002874 2081
+#> 3 Gene3 0.707714763953083 2387
+#> 4 Gene4 0.15575800464631 995
+#> 5 Gene5 0.0181238728394951 2635
+#> 6 Gene6 1.30100599611438 2357</div><div class='input'># Sample method (human coding genes)
</div><span class='co'># NOT RUN {</span>
<span class='fu'>library</span>(<span class='no'>TxDb.Hsapiens.UCSC.hg19.knownGene</span>)
<span class='fu'>library</span>(<span class='no'>GenomicFeatures</span>)
@@ -199,5 +220,8 @@ vector.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/bridge.html b/docs/reference/bridge.html
index c92b62b3c3afd42fa89abb6b941eb1b2710eaa8f..4c3f93eb85573c80f6fa980b4d0316f0f4ad84b5 100644
--- a/docs/reference/bridge.html
+++ b/docs/reference/bridge.html
@@ -18,13 +18,28 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Brownian bridge — bridge" />
+
+<meta property="og:description" content="Calculate a smoothed Brownian bridge between two points. A Brownian bridge is
+a random walk with fixed end points." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +49,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +72,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +87,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +105,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,20 +113,24 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Brownian bridge</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/splat-simulate.R'><code>R/splat-simulate.R</code></a></small>
+ <div class="hidden name"><code>bridge.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Calculate a smoothed Brownian bridge between two points. A Brownian bridge is
a random walk with fixed end points.</p>
+ </div>
<pre class="usage"><span class='fu'>bridge</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>y</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>N</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>sigma.fac</span> <span class='kw'>=</span> <span class='fl'>0.8</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -162,5 +184,8 @@ a random walk with fixed end points.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/compareSCEs.html b/docs/reference/compareSCEs.html
index 5d6fb33d7c9a2d60c5aca7caf642ef8025046a3c..663faca6b09e5a0dd9137d91902566b92386fce1 100644
--- a/docs/reference/compareSCEs.html
+++ b/docs/reference/compareSCEs.html
@@ -18,13 +18,28 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Compare SingleCellExperiment objects — compareSCEs" />
+
+<meta property="og:description" content="Combine the data from several SingleCellExperiment objects and produce some
+basic plots comparing them." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +49,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +72,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +87,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +105,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,21 +113,25 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Compare SingleCellExperiment objects</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/compare.R'><code>R/compare.R</code></a></small>
+ <div class="hidden name"><code>compareSCEs.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Combine the data from several SingleCellExperiment objects and produce some
basic plots comparing them.</p>
+ </div>
<pre class="usage"><span class='fu'>compareSCEs</span>(<span class='no'>sces</span>, <span class='kw'>point.size</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>point.alpha</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>fits</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>colours</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -141,7 +163,8 @@ compare.</p></td>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
- <p>The returned list has three items:</p><dl class='dl-horizontal'>
+ <p>The returned list has three items:</p>
+<dl class='dl-horizontal'>
<dt><code>FeatureData</code></dt><dd><p>Combined feature data from the provided
SingleCellExperiments.</p></dd>
<dt><code>PhenoData</code></dt><dd><p>Combined pheno data from the provided
@@ -163,14 +186,14 @@ compare.</p></td>
</dl></p></dd>
</dl>
<p>The plots returned by this function are created using
-<code><a href='http://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></code> and are only a sample of the kind of plots you
+<code><a href='ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></code> and are only a sample of the kind of plots you
might like to consider. The data used to create these plots is also returned
and should be in the correct format to allow you to create further plots
-using <code><a href='http://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></code>.</p>
+using <code><a href='ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></code>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts..</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>comparison</span> <span class='kw'><-</span> <span class='fu'>compareSCEs</span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>))</div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
+ <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>comparison</span> <span class='kw'><-</span> <span class='fu'>compareSCEs</span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>))</div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
#> <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
#> <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='input'><span class='fu'>names</span>(<span class='no'>comparison</span>)</div><div class='output co'>#> [1] "FeatureData" "PhenoData" "Plots" </div><div class='input'><span class='fu'>names</span>(<span class='no'>comparison</span>$<span class='no'>Plots</span>)</div><div class='output co'>#> [1] "Means" "Variances" "MeanVar" "LibrarySizes" "ZerosGene"
#> [6] "ZerosCell" "MeanZeros" </div></pre>
@@ -202,5 +225,8 @@ using <code><a href='http://www.rdocumentation.org/packages/ggplot2/topics/ggplo
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/diffSCEs.html b/docs/reference/diffSCEs.html
index 6ee0aef841bcaf1a554fe2cdd8fb988f46571466..30744dc31501007f995b9ff7e1e51735426a61ae 100644
--- a/docs/reference/diffSCEs.html
+++ b/docs/reference/diffSCEs.html
@@ -18,13 +18,28 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Diff SingleCellExperiment objects — diffSCEs" />
+
+<meta property="og:description" content="Combine the data from several SingleCellExperiment objects and produce some
+basic plots comparing them to a reference." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +49,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +72,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +87,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +105,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,21 +113,25 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Diff SingleCellExperiment objects</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/compare.R'><code>R/compare.R</code></a></small>
+ <div class="hidden name"><code>diffSCEs.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Combine the data from several SingleCellExperiment objects and produce some
basic plots comparing them to a reference.</p>
+ </div>
<pre class="usage"><span class='fu'>diffSCEs</span>(<span class='no'>sces</span>, <span class='no'>ref</span>, <span class='kw'>point.size</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>point.alpha</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>fits</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>colours</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -152,7 +174,8 @@ SingleCellExperiment to have the same dimensions. Properties are compared by
ranks, for example when comparing the means the values are ordered and the
differences between the reference and another dataset plotted. A series of
Q-Q plots are also returned.</p>
-<p>The returned list has five items:</p><dl class='dl-horizontal'>
+<p>The returned list has five items:</p>
+<dl class='dl-horizontal'>
<dt><code>Reference</code></dt><dd><p>The SingleCellExperiment used as the reference.</p></dd>
<dt><code>FeatureData</code></dt><dd><p>Combined feature data from the provided
SingleCellExperiments.</p></dd>
@@ -185,14 +208,14 @@ Q-Q plots are also returned.</p>
</dl></p></dd>
</dl>
<p>The plots returned by this function are created using
-<code><a href='http://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></code> and are only a sample of the kind of plots you
+<code><a href='ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></code> and are only a sample of the kind of plots you
might like to consider. The data used to create these plots is also returned
and should be in the correct format to allow you to create further plots
-using <code><a href='http://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></code>.</p>
+using <code><a href='ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></code>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts..</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'>diffSCEs</span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)</div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
+ <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'>diffSCEs</span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)</div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
#> <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
#> <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='input'><span class='fu'>names</span>(<span class='no'>difference</span>)</div><div class='output co'>#> [1] "Reference" "FeatureData" "PhenoData" "Plots" "QQPlots" </div><div class='input'><span class='fu'>names</span>(<span class='no'>difference</span>$<span class='no'>Plots</span>)</div><div class='output co'>#> [1] "Means" "Variances" "MeanVar" "LibrarySizes" "ZerosGene"
#> [6] "ZerosCell" "MeanZeros" </div></pre>
@@ -224,5 +247,8 @@ using <code><a href='http://www.rdocumentation.org/packages/ggplot2/topics/ggplo
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/expandParams.html b/docs/reference/expandParams.html
index d6ee6f7e5d5c9e9208e9a900b68f654285d69ff6..960dcab37dd7426ec29f1ad517edfdef1e80d9f6 100644
--- a/docs/reference/expandParams.html
+++ b/docs/reference/expandParams.html
@@ -18,13 +18,28 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Expand parameters — expandParams" />
+
+<meta property="og:description" content="Expand the parameters that can be vectors so that they are the same length as
+the number of groups." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +49,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +72,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +87,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +105,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,16 +113,20 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Expand parameters</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/AllGenerics.R'><code>R/AllGenerics.R</code></a>, <a href='https://github.com/Oshlack/splatter/blob/master/R/BASiCSParams-methods.R'><code>R/BASiCSParams-methods.R</code></a>, <a href='https://github.com/Oshlack/splatter/blob/master/R/LunParams-methods.R'><code>R/LunParams-methods.R</code></a>, and 2 more</small>
+ <div class="hidden name"><code>expandParams.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Expand the parameters that can be vectors so that they are the same length as
the number of groups.</p>
+ </div>
<pre class="usage"><span class='fu'>expandParams</span>(<span class='no'>object</span>, <span class='no'>...</span>)
@@ -117,7 +139,7 @@ the number of groups.</p>
<span class='co'># S4 method for SplatParams</span>
<span class='fu'>expandParams</span>(<span class='no'>object</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -159,5 +181,8 @@ the number of groups.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/getLNormFactors.html b/docs/reference/getLNormFactors.html
index c157131adcfb86d85f09ad4d1e936901495cec37..0eae1399a1620b3bf8dc864e242701b0efa77161 100644
--- a/docs/reference/getLNormFactors.html
+++ b/docs/reference/getLNormFactors.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Get log-normal factors — getLNormFactors" />
+
+<meta property="og:description" content="Randomly generate multiplication factors from a log-normal distribution." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,19 +112,23 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Get log-normal factors</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/splat-simulate.R'><code>R/splat-simulate.R</code></a></small>
+ <div class="hidden name"><code>getLNormFactors.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Randomly generate multiplication factors from a log-normal distribution.</p>
+ </div>
<pre class="usage"><span class='fu'>getLNormFactors</span>(<span class='no'>n.facs</span>, <span class='no'>sel.prob</span>, <span class='no'>neg.prob</span>, <span class='no'>fac.loc</span>, <span class='no'>fac.scale</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -162,5 +183,8 @@ from 1.</p></td>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/getParam.html b/docs/reference/getParam.html
index c606e868d166a0ebe075ebb8c5aacd5f176c8439..c2c7a3877a4c677283f4b9a1dcfb5ebd9973db57 100644
--- a/docs/reference/getParam.html
+++ b/docs/reference/getParam.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Get a parameter — getParam" />
+
+<meta property="og:description" content="Accessor function for getting parameter values." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,22 +112,26 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Get a parameter</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/AllGenerics.R'><code>R/AllGenerics.R</code></a>, <a href='https://github.com/Oshlack/splatter/blob/master/R/Params-methods.R'><code>R/Params-methods.R</code></a></small>
+ <div class="hidden name"><code>getParam.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Accessor function for getting parameter values.</p>
+ </div>
<pre class="usage"><span class='fu'>getParam</span>(<span class='no'>object</span>, <span class='no'>name</span>)
<span class='co'># S4 method for Params</span>
<span class='fu'>getParam</span>(<span class='no'>object</span>, <span class='no'>name</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -158,5 +179,8 @@
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/getParams.html b/docs/reference/getParams.html
index 7a1af5951c39a397004d7e3dd55687a6169dc121..8c2f7bc0769398cf372ecb1fb7b076693eed859a 100644
--- a/docs/reference/getParams.html
+++ b/docs/reference/getParams.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Get parameters — getParams" />
+
+<meta property="og:description" content="Get multiple parameter values from a Params object." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,19 +112,23 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Get parameters</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/params-functions.R'><code>R/params-functions.R</code></a></small>
+ <div class="hidden name"><code>getParams.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Get multiple parameter values from a Params object.</p>
+ </div>
<pre class="usage"><span class='fu'>getParams</span>(<span class='no'>params</span>, <span class='no'>names</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -162,5 +183,8 @@
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/getPathOrder.html b/docs/reference/getPathOrder.html
index 87b35c87ccf5e2be63e7efe4129967be7be88326..3b14391f0f30718d863e20e8a01e2d50bc76d74e 100644
--- a/docs/reference/getPathOrder.html
+++ b/docs/reference/getPathOrder.html
@@ -18,13 +18,28 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Get path order — getPathOrder" />
+
+<meta property="og:description" content="Identify the correct order to process paths so that preceding paths have
+already been simulated." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +49,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +72,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +87,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +105,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,20 +113,24 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Get path order</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/splat-simulate.R'><code>R/splat-simulate.R</code></a></small>
+ <div class="hidden name"><code>getPathOrder.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Identify the correct order to process paths so that preceding paths have
already been simulated.</p>
+ </div>
<pre class="usage"><span class='fu'>getPathOrder</span>(<span class='no'>path.from</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -147,5 +169,8 @@ from.</p></td>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/index.html b/docs/reference/index.html
index a561dd4f0cf82e9b56ef046471180aa4cd451200..494a3e562a804eff203df6fa980117ff0273678a 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -18,13 +18,24 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Function reference" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +45,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +68,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +83,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +101,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,500 +109,496 @@
</header>
- <div class="row">
- <div class="col-md-9">
+<div class="row">
+ <div class="contents col-md-9">
<div class="page-header">
- <h1>
- Reference
- <small>version 1.5.0</small>
- </h1>
+ <h1>Reference</h1>
</div>
- <div class="contents">
- <table class="ref-index">
-
- <colgroup>
- <col class="alias" />
- <col class="title" />
- </colgroup>
-
- <tbody>
- <tr>
- <th colspan="2">
- <h2 id="section-parameters" class="hasAnchor"><a href="#section-parameters" class="anchor"></a>Parameters</h2>
- <p class="section-desc"><p>Parameters functions and classes</p></p>
- </th>
- </tr>
- <tr>
- <!-- -->
- <td>
- <p><code><a href="newParams.html">newBASiCSParams</a></code> <code><a href="newParams.html">newLun2Params</a></code> <code><a href="newParams.html">newLunParams</a></code> <code><a href="newParams.html">newMFAParams</a></code> <code><a href="newParams.html">newPhenoParams</a></code> <code><a href="newParams.html">newSCDDParams</a></code> <code><a href="newParams.html">newSimpleParams</a></code> <code><a href="newParams.html">newSparseDCParams</a></code> <code><a href="newParams.html">newSplatParams</a></code> <code><a href="newParams.html">newZINBParams</a></code> </p>
- </td>
- <td><p>New Params</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="getParam.html">getParam</a></code> </p>
- </td>
- <td><p>Get a parameter</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="getParams.html">getParams</a></code> </p>
- </td>
- <td><p>Get parameters</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="setParam.html">setParam</a></code> </p>
- </td>
- <td><p>Set a parameter</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="setParams.html">setParams</a></code> </p>
- </td>
- <td><p>Set parameters</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="BASiCSParams.html">BASiCSParams</a></code> </p>
- </td>
- <td><p>The BASiCSParams class</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="Lun2Params.html">Lun2Params</a></code> </p>
- </td>
- <td><p>The Lun2Params class</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="LunParams.html">LunParams</a></code> </p>
- </td>
- <td><p>The LunParams class</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="MFAParams.html">MFAParams</a></code> </p>
- </td>
- <td><p>The MFAParams class</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="Params.html">Params</a></code> </p>
- </td>
- <td><p>The Params virtual class</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="PhenoParams.html">PhenoParams</a></code> </p>
- </td>
- <td><p>The PhenoParams class</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="SCDDParams.html">SCDDParams</a></code> </p>
- </td>
- <td><p>The SCDDParams class</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="SimpleParams.html">SimpleParams</a></code> </p>
- </td>
- <td><p>The SimpleParams class</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="SplatParams.html">SplatParams</a></code> </p>
- </td>
- <td><p>The SplatParams class</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="SparseDCParams.html">SparseDCParams</a></code> </p>
- </td>
- <td><p>The SparseDCParams class</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="ZINBParams.html">ZINBParams</a></code> </p>
- </td>
- <td><p>The ZINBParams class</p></td>
- </tr>
- </tbody><tbody>
- <tr>
- <th colspan="2">
- <h2 id="section-estimation" class="hasAnchor"><a href="#section-estimation" class="anchor"></a>Estimation</h2>
- <p class="section-desc"><p>Functions for estimating parameters</p></p>
- </th>
- </tr>
- <tr>
- <!-- -->
- <td>
- <p><code><a href="BASiCSEstimate.html">BASiCSEstimate</a></code> </p>
- </td>
- <td><p>Estimate BASiCS simulation parameters</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="lun2Estimate.html">lun2Estimate</a></code> </p>
- </td>
- <td><p>Estimate Lun2 simulation parameters</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="lunEstimate.html">lunEstimate</a></code> </p>
- </td>
- <td><p>Estimate Lun simulation parameters</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="mfaEstimate.html">mfaEstimate</a></code> </p>
- </td>
- <td><p>Estimate mfa simulation parameters</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="phenoEstimate.html">phenoEstimate</a></code> </p>
- </td>
- <td><p>Estimate PhenoPath simulation parameters</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="scDDEstimate.html">scDDEstimate</a></code> </p>
- </td>
- <td><p>Estimate scDD simulation parameters</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="simpleEstimate.html">simpleEstimate</a></code> </p>
- </td>
- <td><p>Estimate simple simulation parameters</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="splatEstBCV.html">splatEstBCV</a></code> </p>
- </td>
- <td><p>Estimate Splat Biological Coefficient of Variation parameters</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="splatEstDropout.html">splatEstDropout</a></code> </p>
- </td>
- <td><p>Estimate Splat dropout parameters</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="splatEstimate.html">splatEstimate</a></code> </p>
- </td>
- <td><p>Estimate Splat simulation parameters</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="splatEstLib.html">splatEstLib</a></code> </p>
- </td>
- <td><p>Estimate Splat library size parameters</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="splatEstMean.html">splatEstMean</a></code> </p>
- </td>
- <td><p>Estimate Splat mean parameters</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="splatEstOutlier.html">splatEstOutlier</a></code> </p>
- </td>
- <td><p>Estimate Splat expression outlier parameters</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="sparseDCEstimate.html">sparseDCEstimate</a></code> </p>
- </td>
- <td><p>Estimate SparseDC simulation parameters</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="zinbEstimate.html">zinbEstimate</a></code> </p>
- </td>
- <td><p>Estimate ZINB-WaVE simulation parameters</p></td>
- </tr>
- </tbody><tbody>
- <tr>
- <th colspan="2">
- <h2 id="section-simulation" class="hasAnchor"><a href="#section-simulation" class="anchor"></a>Simulation</h2>
- <p class="section-desc"><p>Functions for simulating datasets</p></p>
- </th>
- </tr>
- <tr>
- <!-- -->
- <td>
- <p><code><a href="BASiCSSimulate.html">BASiCSSimulate</a></code> </p>
- </td>
- <td><p>BASiCS simulation</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="lun2Simulate.html">lun2Simulate</a></code> </p>
- </td>
- <td><p>Lun2 simulation</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="lunSimulate.html">lunSimulate</a></code> </p>
- </td>
- <td><p>Lun simulation</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="mfaSimulate.html">mfaSimulate</a></code> </p>
- </td>
- <td><p>MFA simulation</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="phenoSimulate.html">phenoSimulate</a></code> </p>
- </td>
- <td><p>PhenoPath simulation</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="scDDSimulate.html">scDDSimulate</a></code> </p>
- </td>
- <td><p>scDD simulation</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="simpleSimulate.html">simpleSimulate</a></code> </p>
- </td>
- <td><p>Simple simulation</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="splatSimBatchCellMeans.html">splatSimBatchCellMeans</a></code> </p>
- </td>
- <td><p>Simulate batch means</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="splatSimBatchEffects.html">splatSimBatchEffects</a></code> </p>
- </td>
- <td><p>Simulate batch effects</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="splatSimBCVMeans.html">splatSimBCVMeans</a></code> </p>
- </td>
- <td><p>Simulate BCV means</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="splatSimCellMeans.html">splatSimSingleCellMeans</a></code> <code><a href="splatSimCellMeans.html">splatSimGroupCellMeans</a></code> <code><a href="splatSimCellMeans.html">splatSimPathCellMeans</a></code> </p>
- </td>
- <td><p>Simulate cell means</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="splatSimDE.html">splatSimGroupDE</a></code> <code><a href="splatSimDE.html">splatSimPathDE</a></code> </p>
- </td>
- <td><p>Simulate group differential expression</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="splatSimDropout.html">splatSimDropout</a></code> </p>
- </td>
- <td><p>Simulate dropout</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="splatSimGeneMeans.html">splatSimGeneMeans</a></code> </p>
- </td>
- <td><p>Simulate gene means</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="splatSimLibSizes.html">splatSimLibSizes</a></code> </p>
- </td>
- <td><p>Simulate library sizes</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="splatSimTrueCounts.html">splatSimTrueCounts</a></code> </p>
- </td>
- <td><p>Simulate true counts</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="splatSimulate.html">splatSimulate</a></code> <code><a href="splatSimulate.html">splatSimulateSingle</a></code> <code><a href="splatSimulate.html">splatSimulateGroups</a></code> <code><a href="splatSimulate.html">splatSimulatePaths</a></code> </p>
- </td>
- <td><p>Splat simulation</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="sparseDCSimulate.html">sparseDCSimulate</a></code> </p>
- </td>
- <td><p>SparseDC simulation</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="zinbSimulate.html">zinbSimulate</a></code> </p>
- </td>
- <td><p>ZINB-WaVE simulation</p></td>
- </tr>
- </tbody><tbody>
- <tr>
- <th colspan="2">
- <h2 id="section-comparison-functions" class="hasAnchor"><a href="#section-comparison-functions" class="anchor"></a>Comparison functions</h2>
- <p class="section-desc"><p>Functions for comparing datasets</p></p>
- </th>
- </tr>
- <tr>
- <!-- -->
- <td>
- <p><code><a href="compareSCEs.html">compareSCEs</a></code> </p>
- </td>
- <td><p>Compare SingleCellExperiment objects</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="diffSCEs.html">diffSCEs</a></code> </p>
- </td>
- <td><p>Diff SingleCellExperiment objects</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="makeCompPanel.html">makeCompPanel</a></code> </p>
- </td>
- <td><p>Make comparison panel</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="makeDiffPanel.html">makeDiffPanel</a></code> </p>
- </td>
- <td><p>Make difference panel</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="makeOverallPanel.html">makeOverallPanel</a></code> </p>
- </td>
- <td><p>Make overall panel</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="summariseDiff.html">summariseDiff</a></code> </p>
- </td>
- <td><p>Summarise diffSCESs</p></td>
- </tr>
- </tbody><tbody>
- <tr>
- <th colspan="2">
- <h2 id="section-other-exported-functions" class="hasAnchor"><a href="#section-other-exported-functions" class="anchor"></a>Other exported functions</h2>
- <p class="section-desc"><p>Additional functions exported by Splatter</p></p>
- </th>
- </tr>
- <tr>
- <!-- -->
- <td>
- <p><code><a href="addFeatureStats.html">addFeatureStats</a></code> </p>
- </td>
- <td><p>Add feature statistics</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="addGeneLengths.html">addGeneLengths</a></code> </p>
- </td>
- <td><p>Add gene lengths</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="listSims.html">listSims</a></code> </p>
- </td>
- <td><p>List simulations</p></td>
- </tr>
- </tbody><tbody>
- <tr>
- <th colspan="2">
- <h2 id="section-internals" class="hasAnchor"><a href="#section-internals" class="anchor"></a>Internals</h2>
- <p class="section-desc"><p>Internal functions and helpers</p></p>
- </th>
- </tr>
- <tr>
- <!-- -->
- <td>
- <p><code><a href="bridge.html">bridge</a></code> </p>
- </td>
- <td><p>Brownian bridge</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="expandParams.html">expandParams</a></code> </p>
- </td>
- <td><p>Expand parameters</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="getLNormFactors.html">getLNormFactors</a></code> </p>
- </td>
- <td><p>Get log-normal factors</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="getPathOrder.html">getPathOrder</a></code> </p>
- </td>
- <td><p>Get path order</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="logistic.html">logistic</a></code> </p>
- </td>
- <td><p>Logistic function</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="rbindMatched.html">rbindMatched</a></code> </p>
- </td>
- <td><p>Bind rows (matched)</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="setParamsUnchecked.html">setParamsUnchecked</a></code> </p>
- </td>
- <td><p>Set parameters UNCHECKED</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="setParamUnchecked.html">setParamUnchecked</a></code> </p>
- </td>
- <td><p>Set a parameter UNCHECKED</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="showDFs.html">showDFs</a></code> </p>
- </td>
- <td><p>Show data.frame</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="showPP.html">showPP</a></code> </p>
- </td>
- <td><p>Show pretty print</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="showValues.html">showValues</a></code> </p>
- </td>
- <td><p>Show vales</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="winsorize.html">winsorize</a></code> </p>
- </td>
- <td><p>Winsorize vector</p></td>
- </tr>
- </tbody>
- </table>
- </div>
+ <table class="ref-index">
+
+ <colgroup>
+
+ <col class="alias" />
+ <col class="title" />
+ </colgroup>
+
+ <tbody>
+ <tr>
+ <th colspan="2">
+ <h2 id="section-parameters" class="hasAnchor"><a href="#section-parameters" class="anchor"></a>Parameters</h2>
+ <p class="section-desc"><p>Parameters functions and classes</p></p>
+ </th>
+ </tr>
+ <tr>
+
+ <td>
+ <p><code><a href="newParams.html">newBASiCSParams()</a></code> <code><a href="newParams.html">newLun2Params()</a></code> <code><a href="newParams.html">newLunParams()</a></code> <code><a href="newParams.html">newMFAParams()</a></code> <code><a href="newParams.html">newPhenoParams()</a></code> <code><a href="newParams.html">newSCDDParams()</a></code> <code><a href="newParams.html">newSimpleParams()</a></code> <code><a href="newParams.html">newSparseDCParams()</a></code> <code><a href="newParams.html">newSplatParams()</a></code> <code><a href="newParams.html">newZINBParams()</a></code> </p>
+ </td>
+ <td><p>New Params</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="getParam.html">getParam()</a></code> </p>
+ </td>
+ <td><p>Get a parameter</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="getParams.html">getParams()</a></code> </p>
+ </td>
+ <td><p>Get parameters</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="setParam.html">setParam()</a></code> </p>
+ </td>
+ <td><p>Set a parameter</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="setParams.html">setParams()</a></code> </p>
+ </td>
+ <td><p>Set parameters</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="BASiCSParams.html">BASiCSParams</a></code> </p>
+ </td>
+ <td><p>The BASiCSParams class</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="Lun2Params.html">Lun2Params</a></code> </p>
+ </td>
+ <td><p>The Lun2Params class</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="LunParams.html">LunParams</a></code> </p>
+ </td>
+ <td><p>The LunParams class</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="MFAParams.html">MFAParams</a></code> </p>
+ </td>
+ <td><p>The MFAParams class</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="Params.html">Params</a></code> </p>
+ </td>
+ <td><p>The Params virtual class</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="PhenoParams.html">PhenoParams</a></code> </p>
+ </td>
+ <td><p>The PhenoParams class</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="SCDDParams.html">SCDDParams</a></code> </p>
+ </td>
+ <td><p>The SCDDParams class</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="SimpleParams.html">SimpleParams</a></code> </p>
+ </td>
+ <td><p>The SimpleParams class</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="SplatParams.html">SplatParams</a></code> </p>
+ </td>
+ <td><p>The SplatParams class</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="SparseDCParams.html">SparseDCParams</a></code> </p>
+ </td>
+ <td><p>The SparseDCParams class</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="ZINBParams.html">ZINBParams</a></code> </p>
+ </td>
+ <td><p>The ZINBParams class</p></td>
+ </tr>
+ </tbody><tbody>
+ <tr>
+ <th colspan="2">
+ <h2 id="section-estimation" class="hasAnchor"><a href="#section-estimation" class="anchor"></a>Estimation</h2>
+ <p class="section-desc"><p>Functions for estimating parameters</p></p>
+ </th>
+ </tr>
+ <tr>
+
+ <td>
+ <p><code><a href="BASiCSEstimate.html">BASiCSEstimate()</a></code> </p>
+ </td>
+ <td><p>Estimate BASiCS simulation parameters</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="lun2Estimate.html">lun2Estimate()</a></code> </p>
+ </td>
+ <td><p>Estimate Lun2 simulation parameters</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="lunEstimate.html">lunEstimate()</a></code> </p>
+ </td>
+ <td><p>Estimate Lun simulation parameters</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="mfaEstimate.html">mfaEstimate()</a></code> </p>
+ </td>
+ <td><p>Estimate mfa simulation parameters</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="phenoEstimate.html">phenoEstimate()</a></code> </p>
+ </td>
+ <td><p>Estimate PhenoPath simulation parameters</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="scDDEstimate.html">scDDEstimate()</a></code> </p>
+ </td>
+ <td><p>Estimate scDD simulation parameters</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="simpleEstimate.html">simpleEstimate()</a></code> </p>
+ </td>
+ <td><p>Estimate simple simulation parameters</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="splatEstBCV.html">splatEstBCV()</a></code> </p>
+ </td>
+ <td><p>Estimate Splat Biological Coefficient of Variation parameters</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="splatEstDropout.html">splatEstDropout()</a></code> </p>
+ </td>
+ <td><p>Estimate Splat dropout parameters</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="splatEstimate.html">splatEstimate()</a></code> </p>
+ </td>
+ <td><p>Estimate Splat simulation parameters</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="splatEstLib.html">splatEstLib()</a></code> </p>
+ </td>
+ <td><p>Estimate Splat library size parameters</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="splatEstMean.html">splatEstMean()</a></code> </p>
+ </td>
+ <td><p>Estimate Splat mean parameters</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="splatEstOutlier.html">splatEstOutlier()</a></code> </p>
+ </td>
+ <td><p>Estimate Splat expression outlier parameters</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="sparseDCEstimate.html">sparseDCEstimate()</a></code> </p>
+ </td>
+ <td><p>Estimate SparseDC simulation parameters</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="zinbEstimate.html">zinbEstimate()</a></code> </p>
+ </td>
+ <td><p>Estimate ZINB-WaVE simulation parameters</p></td>
+ </tr>
+ </tbody><tbody>
+ <tr>
+ <th colspan="2">
+ <h2 id="section-simulation" class="hasAnchor"><a href="#section-simulation" class="anchor"></a>Simulation</h2>
+ <p class="section-desc"><p>Functions for simulating datasets</p></p>
+ </th>
+ </tr>
+ <tr>
+
+ <td>
+ <p><code><a href="BASiCSSimulate.html">BASiCSSimulate()</a></code> </p>
+ </td>
+ <td><p>BASiCS simulation</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="lun2Simulate.html">lun2Simulate()</a></code> </p>
+ </td>
+ <td><p>Lun2 simulation</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="lunSimulate.html">lunSimulate()</a></code> </p>
+ </td>
+ <td><p>Lun simulation</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="mfaSimulate.html">mfaSimulate()</a></code> </p>
+ </td>
+ <td><p>MFA simulation</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="phenoSimulate.html">phenoSimulate()</a></code> </p>
+ </td>
+ <td><p>PhenoPath simulation</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="scDDSimulate.html">scDDSimulate()</a></code> </p>
+ </td>
+ <td><p>scDD simulation</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="simpleSimulate.html">simpleSimulate()</a></code> </p>
+ </td>
+ <td><p>Simple simulation</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="splatSimBatchCellMeans.html">splatSimBatchCellMeans()</a></code> </p>
+ </td>
+ <td><p>Simulate batch means</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="splatSimBatchEffects.html">splatSimBatchEffects()</a></code> </p>
+ </td>
+ <td><p>Simulate batch effects</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="splatSimBCVMeans.html">splatSimBCVMeans()</a></code> </p>
+ </td>
+ <td><p>Simulate BCV means</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="splatSimCellMeans.html">splatSimSingleCellMeans()</a></code> <code><a href="splatSimCellMeans.html">splatSimGroupCellMeans()</a></code> <code><a href="splatSimCellMeans.html">splatSimPathCellMeans()</a></code> </p>
+ </td>
+ <td><p>Simulate cell means</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="splatSimDE.html">splatSimGroupDE()</a></code> <code><a href="splatSimDE.html">splatSimPathDE()</a></code> </p>
+ </td>
+ <td><p>Simulate group differential expression</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="splatSimDropout.html">splatSimDropout()</a></code> </p>
+ </td>
+ <td><p>Simulate dropout</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="splatSimGeneMeans.html">splatSimGeneMeans()</a></code> </p>
+ </td>
+ <td><p>Simulate gene means</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="splatSimLibSizes.html">splatSimLibSizes()</a></code> </p>
+ </td>
+ <td><p>Simulate library sizes</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="splatSimTrueCounts.html">splatSimTrueCounts()</a></code> </p>
+ </td>
+ <td><p>Simulate true counts</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="splatSimulate.html">splatSimulate()</a></code> <code><a href="splatSimulate.html">splatSimulateSingle()</a></code> <code><a href="splatSimulate.html">splatSimulateGroups()</a></code> <code><a href="splatSimulate.html">splatSimulatePaths()</a></code> </p>
+ </td>
+ <td><p>Splat simulation</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="sparseDCSimulate.html">sparseDCSimulate()</a></code> </p>
+ </td>
+ <td><p>SparseDC simulation</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="zinbSimulate.html">zinbSimulate()</a></code> </p>
+ </td>
+ <td><p>ZINB-WaVE simulation</p></td>
+ </tr>
+ </tbody><tbody>
+ <tr>
+ <th colspan="2">
+ <h2 id="section-comparison-functions" class="hasAnchor"><a href="#section-comparison-functions" class="anchor"></a>Comparison functions</h2>
+ <p class="section-desc"><p>Functions for comparing datasets</p></p>
+ </th>
+ </tr>
+ <tr>
+
+ <td>
+ <p><code><a href="compareSCEs.html">compareSCEs()</a></code> </p>
+ </td>
+ <td><p>Compare SingleCellExperiment objects</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="diffSCEs.html">diffSCEs()</a></code> </p>
+ </td>
+ <td><p>Diff SingleCellExperiment objects</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="makeCompPanel.html">makeCompPanel()</a></code> </p>
+ </td>
+ <td><p>Make comparison panel</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="makeDiffPanel.html">makeDiffPanel()</a></code> </p>
+ </td>
+ <td><p>Make difference panel</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="makeOverallPanel.html">makeOverallPanel()</a></code> </p>
+ </td>
+ <td><p>Make overall panel</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="summariseDiff.html">summariseDiff()</a></code> </p>
+ </td>
+ <td><p>Summarise diffSCESs</p></td>
+ </tr>
+ </tbody><tbody>
+ <tr>
+ <th colspan="2">
+ <h2 id="section-other-exported-functions" class="hasAnchor"><a href="#section-other-exported-functions" class="anchor"></a>Other exported functions</h2>
+ <p class="section-desc"><p>Additional functions exported by Splatter</p></p>
+ </th>
+ </tr>
+ <tr>
+
+ <td>
+ <p><code><a href="addFeatureStats.html">addFeatureStats()</a></code> </p>
+ </td>
+ <td><p>Add feature statistics</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="addGeneLengths.html">addGeneLengths()</a></code> </p>
+ </td>
+ <td><p>Add gene lengths</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="listSims.html">listSims()</a></code> </p>
+ </td>
+ <td><p>List simulations</p></td>
+ </tr>
+ </tbody><tbody>
+ <tr>
+ <th colspan="2">
+ <h2 id="section-internals" class="hasAnchor"><a href="#section-internals" class="anchor"></a>Internals</h2>
+ <p class="section-desc"><p>Internal functions and helpers</p></p>
+ </th>
+ </tr>
+ <tr>
+
+ <td>
+ <p><code><a href="bridge.html">bridge()</a></code> </p>
+ </td>
+ <td><p>Brownian bridge</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="expandParams.html">expandParams()</a></code> </p>
+ </td>
+ <td><p>Expand parameters</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="getLNormFactors.html">getLNormFactors()</a></code> </p>
+ </td>
+ <td><p>Get log-normal factors</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="getPathOrder.html">getPathOrder()</a></code> </p>
+ </td>
+ <td><p>Get path order</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="logistic.html">logistic()</a></code> </p>
+ </td>
+ <td><p>Logistic function</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="rbindMatched.html">rbindMatched()</a></code> </p>
+ </td>
+ <td><p>Bind rows (matched)</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="setParamsUnchecked.html">setParamsUnchecked()</a></code> </p>
+ </td>
+ <td><p>Set parameters UNCHECKED</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="setParamUnchecked.html">setParamUnchecked()</a></code> </p>
+ </td>
+ <td><p>Set a parameter UNCHECKED</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="showDFs.html">showDFs()</a></code> </p>
+ </td>
+ <td><p>Show data.frame</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="showPP.html">showPP()</a></code> </p>
+ </td>
+ <td><p>Show pretty print</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="showValues.html">showValues()</a></code> </p>
+ </td>
+ <td><p>Show vales</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="winsorize.html">winsorize()</a></code> </p>
+ </td>
+ <td><p>Winsorize vector</p></td>
+ </tr>
+ </tbody>
+ </table>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
@@ -616,5 +626,8 @@
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/listSims.html b/docs/reference/listSims.html
index df9e49eb61506eef825880d258b5ef5db44f9d2e..10d46c20e5a00beb47fbb18633a69a92fea548ed 100644
--- a/docs/reference/listSims.html
+++ b/docs/reference/listSims.html
@@ -18,13 +18,28 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="List simulations — listSims" />
+
+<meta property="og:description" content="List all the simulations that are currently available in Splatter with a
+brief description." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +49,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +72,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +87,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +105,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,20 +113,24 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>List simulations</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/listSims.R'><code>R/listSims.R</code></a></small>
+ <div class="hidden name"><code>listSims.Rd</code></div>
</div>
+ <div class="ref-description">
<p>List all the simulations that are currently available in Splatter with a
brief description.</p>
+ </div>
<pre class="usage"><span class='fu'>listSims</span>(<span class='kw'>print</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -204,5 +226,8 @@ displayed.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/logistic.html b/docs/reference/logistic.html
index c599ed5b8848e61f993a2cfa427c8a589e8a019c..b940b0ad1d050f8aef52c509492d852018706767 100644
--- a/docs/reference/logistic.html
+++ b/docs/reference/logistic.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Logistic function — logistic" />
+
+<meta property="og:description" content="Implementation of the logistic function" />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,19 +112,23 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Logistic function</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/utils.R'><code>R/utils.R</code></a></small>
+ <div class="hidden name"><code>logistic.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Implementation of the logistic function</p>
+ </div>
<pre class="usage"><span class='fu'>logistic</span>(<span class='no'>x</span>, <span class='no'>x0</span>, <span class='no'>k</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -153,5 +174,8 @@
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/lun2Estimate.html b/docs/reference/lun2Estimate.html
index 0e3a98599e128068c870487799cc385d9b9d1a71..8ece3e84a66ec7851c2849975e614551a4a85ef9 100644
--- a/docs/reference/lun2Estimate.html
+++ b/docs/reference/lun2Estimate.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Estimate Lun2 simulation parameters — lun2Estimate" />
+
+<meta property="og:description" content="Estimate simulation parameters for the Lun2 simulation from a real dataset." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,15 +112,19 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Estimate Lun2 simulation parameters</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/lun2-estimate.R'><code>R/lun2-estimate.R</code></a></small>
+ <div class="hidden name"><code>lun2Estimate.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Estimate simulation parameters for the Lun2 simulation from a real dataset.</p>
+ </div>
<pre class="usage"><span class='fu'>lun2Estimate</span>(<span class='no'>counts</span>, <span class='no'>plates</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newLun2Params</a></span>(), <span class='kw'>min.size</span> <span class='kw'>=</span> <span class='fl'>200</span>,
<span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>())
@@ -117,7 +138,7 @@
<span class='fu'>lun2Estimate</span>(<span class='no'>counts</span>, <span class='no'>plates</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newLun2Params</a></span>(),
<span class='kw'>min.size</span> <span class='kw'>=</span> <span class='fl'>200</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>())</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -198,5 +219,8 @@ single core.</p></td>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/lun2Simulate.html b/docs/reference/lun2Simulate.html
index 5efaca28755ef77fd6759e259d465502508b3219..a2c680d0218402dffd85bf5cb983b21b64d83fab 100644
--- a/docs/reference/lun2Simulate.html
+++ b/docs/reference/lun2Simulate.html
@@ -18,13 +18,29 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Lun2 simulation — lun2Simulate" />
+
+<meta property="og:description" content="Simulate single-cell RNA-seq count data using the method described in Lun
+and Marioni "Overcoming confounding plate effects in differential expression
+analyses of single-cell RNA-seq data"." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +50,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +73,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +88,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +106,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,21 +114,26 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Lun2 simulation</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/lun2-simulate.R'><code>R/lun2-simulate.R</code></a></small>
+ <div class="hidden name"><code>lun2Simulate.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Simulate single-cell RNA-seq count data using the method described in Lun
and Marioni "Overcoming confounding plate effects in differential expression
analyses of single-cell RNA-seq data".</p>
+ </div>
- <pre class="usage"><span class='fu'>lun2Simulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newLun2Params</a></span>(), <span class='kw'>zinb</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
+ <pre class="usage"><span class='fu'>lun2Simulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newLun2Params</a></span>(), <span class='kw'>zinb</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+ <span class='no'>...</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -191,5 +215,8 @@ expression analyses of single-cell RNA-seq data. Biostatistics (2017).</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/lunEstimate.html b/docs/reference/lunEstimate.html
index 576cfe236bf9a12337046ecd3d042094b97e46ee..2844626c1c9c1211985343333010c284cf89a35e 100644
--- a/docs/reference/lunEstimate.html
+++ b/docs/reference/lunEstimate.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Estimate Lun simulation parameters — lunEstimate" />
+
+<meta property="og:description" content="Estimate simulation parameters for the Lun simulation from a real dataset." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,25 +112,30 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Estimate Lun simulation parameters</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/lun-estimate.R'><code>R/lun-estimate.R</code></a></small>
+ <div class="hidden name"><code>lunEstimate.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Estimate simulation parameters for the Lun simulation from a real dataset.</p>
+ </div>
<pre class="usage"><span class='fu'>lunEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newLunParams</a></span>())
<span class='co'># S3 method for SingleCellExperiment</span>
-<span class='fu'>lunEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newLunParams</a></span>())
+<span class='fu'>lunEstimate</span>(<span class='no'>counts</span>,
+ <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newLunParams</a></span>())
<span class='co'># S3 method for matrix</span>
<span class='fu'>lunEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newLunParams</a></span>())</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -140,8 +162,12 @@ for more details on the parameters.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># Load example data</span>
-<span class='fu'>library</span>(<span class='no'>scater</span>)
-<span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+<span class='fu'>library</span>(<span class='no'>scater</span>)</div><div class='output co'>#> <span class='message'>Loading required package: ggplot2</span></div><div class='output co'>#> <span class='message'></span>
+#> <span class='message'>Attaching package: ‘scater’</span></div><div class='output co'>#> <span class='message'>The following object is masked from ‘package:S4Vectors’:</span>
+#> <span class='message'></span>
+#> <span class='message'> rename</span></div><div class='output co'>#> <span class='message'>The following object is masked from ‘package:stats’:</span>
+#> <span class='message'></span>
+#> <span class='message'> filter</span></div><div class='input'><span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>lunEstimate</span>(<span class='no'>sc_example_counts</span>)
<span class='no'>params</span></div><div class='output co'>#> A Params object of class LunParams
@@ -149,7 +175,7 @@ for more details on the parameters.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 171612
+#> 2000 40 667401
#>
#> 9 additional parameters
#>
@@ -197,5 +223,8 @@ for more details on the parameters.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/lunSimulate.html b/docs/reference/lunSimulate.html
index 84ca3dea19be4b33ed29f7e0f7d8c3a79d38462a..f23ba51fdad42d89815464e25612d5d867e9613b 100644
--- a/docs/reference/lunSimulate.html
+++ b/docs/reference/lunSimulate.html
@@ -18,13 +18,29 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Lun simulation — lunSimulate" />
+
+<meta property="og:description" content="Simulate single-cell RNA-seq count data using the method described in Lun,
+Bach and Marioni "Pooling across cells to normalize single-cell RNA
+sequencing data with many zero counts"." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +50,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +73,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +88,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +106,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,21 +114,25 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Lun simulation</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/lun-simulate.R'><code>R/lun-simulate.R</code></a></small>
+ <div class="hidden name"><code>lunSimulate.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Simulate single-cell RNA-seq count data using the method described in Lun,
Bach and Marioni "Pooling across cells to normalize single-cell RNA
sequencing data with many zero counts".</p>
+ </div>
<pre class="usage"><span class='fu'>lunSimulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newLunParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -183,5 +206,8 @@ RNA sequencing data with many zero counts. Genome Biology (2016).</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/makeCompPanel.html b/docs/reference/makeCompPanel.html
index b0184c32a219c0b2a11ab486cd3e0730bc9674a2..5955b69981b7927caba9fb1f2815e96a9dd1c43c 100644
--- a/docs/reference/makeCompPanel.html
+++ b/docs/reference/makeCompPanel.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Make comparison panel — makeCompPanel" />
+
+<meta property="og:description" content="Combine the plots from compareSCEs into a single panel." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,21 +112,25 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Make comparison panel</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/compare.R'><code>R/compare.R</code></a></small>
+ <div class="hidden name"><code>makeCompPanel.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Combine the plots from <code>compareSCEs</code> into a single panel.</p>
+ </div>
- <pre class="usage"><span class='fu'>makeCompPanel</span>(<span class='no'>comp</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"Comparison"</span>, <span class='kw'>labels</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Means"</span>, <span class='st'>"Variance"</span>,
- <span class='st'>"Mean-variance relationship"</span>, <span class='st'>"Library size"</span>, <span class='st'>"Zeros per gene"</span>,
- <span class='st'>"Zeros per cell"</span>, <span class='st'>"Mean-zeros relationship"</span>))</pre>
+ <pre class="usage"><span class='fu'>makeCompPanel</span>(<span class='no'>comp</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"Comparison"</span>, <span class='kw'>labels</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Means"</span>,
+ <span class='st'>"Variance"</span>, <span class='st'>"Mean-variance relationship"</span>, <span class='st'>"Library size"</span>,
+ <span class='st'>"Zeros per gene"</span>, <span class='st'>"Zeros per cell"</span>, <span class='st'>"Mean-zeros relationship"</span>))</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -165,5 +186,8 @@
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/makeDiffPanel.html b/docs/reference/makeDiffPanel.html
index cfabb097a54c05571ccc1ab21f2101d40f3bcbc0..8d139fa6ede801d3e682bd7ff9b9107f8dc7a9f5 100644
--- a/docs/reference/makeDiffPanel.html
+++ b/docs/reference/makeDiffPanel.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Make difference panel — makeDiffPanel" />
+
+<meta property="og:description" content="Combine the plots from diffSCEs into a single panel." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,21 +112,26 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Make difference panel</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/compare.R'><code>R/compare.R</code></a></small>
+ <div class="hidden name"><code>makeDiffPanel.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Combine the plots from <code>diffSCEs</code> into a single panel.</p>
+ </div>
- <pre class="usage"><span class='fu'>makeDiffPanel</span>(<span class='no'>diff</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"Difference comparison"</span>, <span class='kw'>labels</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Means"</span>,
- <span class='st'>"Variance"</span>, <span class='st'>"Library size"</span>, <span class='st'>"Zeros per cell"</span>, <span class='st'>"Zeros per gene"</span>,
- <span class='st'>"Mean-variance relationship"</span>, <span class='st'>"Mean-zeros relationship"</span>))</pre>
+ <pre class="usage"><span class='fu'>makeDiffPanel</span>(<span class='no'>diff</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"Difference comparison"</span>,
+ <span class='kw'>labels</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Means"</span>, <span class='st'>"Variance"</span>, <span class='st'>"Library size"</span>, <span class='st'>"Zeros per cell"</span>,
+ <span class='st'>"Zeros per gene"</span>, <span class='st'>"Mean-variance relationship"</span>,
+ <span class='st'>"Mean-zeros relationship"</span>))</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -165,5 +187,8 @@
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/makeOverallPanel.html b/docs/reference/makeOverallPanel.html
index 09aab89a32d8366e0aef790cad52c96a45f018b0..62731232a3782c8214f6a476dc8d666467bc913b 100644
--- a/docs/reference/makeOverallPanel.html
+++ b/docs/reference/makeOverallPanel.html
@@ -18,13 +18,28 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Make overall panel — makeOverallPanel" />
+
+<meta property="og:description" content="Combine the plots from compSCEs and diffSCEs into a
+single panel." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +49,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +72,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +87,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +105,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,23 +113,27 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Make overall panel</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/compare.R'><code>R/compare.R</code></a></small>
+ <div class="hidden name"><code>makeOverallPanel.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Combine the plots from <code>compSCEs</code> and <code>diffSCEs</code> into a
single panel.</p>
+ </div>
<pre class="usage"><span class='fu'>makeOverallPanel</span>(<span class='no'>comp</span>, <span class='no'>diff</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"Overall comparison"</span>,
<span class='kw'>row.labels</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Means"</span>, <span class='st'>"Variance"</span>, <span class='st'>"Mean-variance relationship"</span>,
<span class='st'>"Library size"</span>, <span class='st'>"Zeros per cell"</span>, <span class='st'>"Zeros per gene"</span>,
<span class='st'>"Mean-zeros relationship"</span>))</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -172,5 +194,8 @@ single panel.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/mfaEstimate.html b/docs/reference/mfaEstimate.html
index eba1a78adae4f72467ca47276ca1f1d551eb706e..3384d70b7a62445b836b6153995157be88e81ffd 100644
--- a/docs/reference/mfaEstimate.html
+++ b/docs/reference/mfaEstimate.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Estimate mfa simulation parameters — mfaEstimate" />
+
+<meta property="og:description" content="Estimate simulation parameters for the mfa simulation from a real dataset." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,25 +112,30 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Estimate mfa simulation parameters</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/mfa-estimate.R'><code>R/mfa-estimate.R</code></a></small>
+ <div class="hidden name"><code>mfaEstimate.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Estimate simulation parameters for the mfa simulation from a real dataset.</p>
+ </div>
<pre class="usage"><span class='fu'>mfaEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newMFAParams</a></span>())
<span class='co'># S3 method for SingleCellExperiment</span>
-<span class='fu'>mfaEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newMFAParams</a></span>())
+<span class='fu'>mfaEstimate</span>(<span class='no'>counts</span>,
+ <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newMFAParams</a></span>())
<span class='co'># S3 method for matrix</span>
<span class='fu'>mfaEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newMFAParams</a></span>())</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -150,7 +172,7 @@ details on the parameters.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 171612
+#> 2000 40 667401
#>
#> 4 additional parameters
#>
@@ -194,5 +216,8 @@ details on the parameters.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/mfaSimulate.html b/docs/reference/mfaSimulate.html
index 2ae55715e72e997799799e0ce24ed991b5635637..4da15e2a8e8706a37645b7f837c742f14ff37172 100644
--- a/docs/reference/mfaSimulate.html
+++ b/docs/reference/mfaSimulate.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="MFA simulation — mfaSimulate" />
+
+<meta property="og:description" content="Simulate a bifurcating pseudotime path using the mfa method." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,19 +112,23 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>MFA simulation</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/mfa-simulate.R'><code>R/mfa-simulate.R</code></a></small>
+ <div class="hidden name"><code>mfaSimulate.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Simulate a bifurcating pseudotime path using the mfa method.</p>
+ </div>
<pre class="usage"><span class='fu'>mfaSimulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newMFAParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -179,5 +200,8 @@ Open Research (2017).</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/newParams.html b/docs/reference/newParams.html
index 8ca19cd443bb4c4b896bb06cc2006544aafc1325..1cdcfed260cac0419053e9d968b822fb992091a8 100644
--- a/docs/reference/newParams.html
+++ b/docs/reference/newParams.html
@@ -18,13 +18,28 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="New Params — newParams" />
+
+<meta property="og:description" content="Create a new Params object. Functions exist for each of the different
+Params subtypes." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +49,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +72,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +87,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +105,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,16 +113,20 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>New Params</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/AllGenerics.R'><code>R/AllGenerics.R</code></a>, <a href='https://github.com/Oshlack/splatter/blob/master/R/BASiCSParams-methods.R'><code>R/BASiCSParams-methods.R</code></a>, <a href='https://github.com/Oshlack/splatter/blob/master/R/Lun2Params-methods.R'><code>R/Lun2Params-methods.R</code></a>, and 9 more</small>
+ <div class="hidden name"><code>newParams.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Create a new Params object. Functions exist for each of the different
Params subtypes.</p>
+ </div>
<pre class="usage"><span class='fu'>newBASiCSParams</span>(<span class='no'>...</span>)
@@ -126,7 +148,7 @@ Params subtypes.</p>
<span class='fu'>newZINBParams</span>(<span class='no'>...</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -169,5 +191,8 @@ Params subtypes.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/phenoEstimate.html b/docs/reference/phenoEstimate.html
index 5e0282edc3d79577126d21153ac1d69929dfc0a7..639dde8f40616f51eba9c1c16d55024213e6fb32 100644
--- a/docs/reference/phenoEstimate.html
+++ b/docs/reference/phenoEstimate.html
@@ -18,13 +18,28 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Estimate PhenoPath simulation parameters — phenoEstimate" />
+
+<meta property="og:description" content="Estimate simulation parameters for the PhenoPath simulation from a real
+dataset." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +49,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +72,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +87,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +105,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,16 +113,20 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Estimate PhenoPath simulation parameters</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/pheno-estimate.R'><code>R/pheno-estimate.R</code></a></small>
+ <div class="hidden name"><code>phenoEstimate.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Estimate simulation parameters for the PhenoPath simulation from a real
dataset.</p>
+ </div>
<pre class="usage"><span class='fu'>phenoEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newPhenoParams</a></span>())
@@ -115,7 +137,7 @@ dataset.</p>
<span class='co'># S3 method for matrix</span>
<span class='fu'>phenoEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newPhenoParams</a></span>())</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -151,7 +173,7 @@ See <code><a href='PhenoParams.html'>PhenoParams</a></code> for more details on
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 171612
+#> 2000 40 667401
#>
#> 4 additional parameters
#>
@@ -187,5 +209,8 @@ See <code><a href='PhenoParams.html'>PhenoParams</a></code> for more details on
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/phenoSimulate.html b/docs/reference/phenoSimulate.html
index 1ed90a231f3802cce94d90af937b9e92176d34de..5920e71a08341d65964d7db0ae062e7cde98da9e 100644
--- a/docs/reference/phenoSimulate.html
+++ b/docs/reference/phenoSimulate.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="PhenoPath simulation — phenoSimulate" />
+
+<meta property="og:description" content="Simulate counts from a pseudotime trajectory using the PhenoPath method." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,19 +112,23 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>PhenoPath simulation</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/pheno-simulate.R'><code>R/pheno-simulate.R</code></a></small>
+ <div class="hidden name"><code>phenoSimulate.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Simulate counts from a pseudotime trajectory using the PhenoPath method.</p>
+ </div>
<pre class="usage"><span class='fu'>phenoSimulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newPhenoParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -182,5 +203,8 @@ and environmental backgrounds across single-cells and populations. bioRxiv
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/rbindMatched.html b/docs/reference/rbindMatched.html
index d88500a9c0d2819ad1c3b1274b0af4719331d59c..0545cb0bee3caa0878198f42c608b64956e9e641 100644
--- a/docs/reference/rbindMatched.html
+++ b/docs/reference/rbindMatched.html
@@ -18,13 +18,28 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Bind rows (matched) — rbindMatched" />
+
+<meta property="og:description" content="Bind the rows of two data frames, keeping only the columns that are common
+to both." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +49,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +72,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +87,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +105,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,20 +113,24 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Bind rows (matched)</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/utils.R'><code>R/utils.R</code></a></small>
+ <div class="hidden name"><code>rbindMatched.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Bind the rows of two data frames, keeping only the columns that are common
to both.</p>
+ </div>
<pre class="usage"><span class='fu'>rbindMatched</span>(<span class='no'>df1</span>, <span class='no'>df2</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -151,5 +173,8 @@ to both.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/scDDEstimate.html b/docs/reference/scDDEstimate.html
index a5b2409a2653605f36dd3a39865a8ae467f49782..3bc5c0891dccbd2f5b7a0e0d801c625ce72bd26a 100644
--- a/docs/reference/scDDEstimate.html
+++ b/docs/reference/scDDEstimate.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Estimate scDD simulation parameters — scDDEstimate" />
+
+<meta property="og:description" content="Estimate simulation parameters for the scDD simulation from a real dataset." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,15 +112,19 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Estimate scDD simulation parameters</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/scDD-estimate.R'><code>R/scDD-estimate.R</code></a></small>
+ <div class="hidden name"><code>scDDEstimate.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Estimate simulation parameters for the scDD simulation from a real dataset.</p>
+ </div>
<pre class="usage"><span class='fu'>scDDEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSCDDParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>(), <span class='no'>...</span>)
@@ -113,14 +134,15 @@
<span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>(), <span class='no'>conditions</span>, <span class='no'>...</span>)
<span class='co'># S3 method for SingleCellExperiment</span>
-<span class='fu'>scDDEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSCDDParams</a></span>(),
- <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>(), <span class='kw'>condition</span> <span class='kw'>=</span> <span class='st'>"condition"</span>, <span class='no'>...</span>)
+<span class='fu'>scDDEstimate</span>(<span class='no'>counts</span>,
+ <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSCDDParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>(),
+ <span class='kw'>condition</span> <span class='kw'>=</span> <span class='st'>"condition"</span>, <span class='no'>...</span>)
<span class='co'># S3 method for default</span>
<span class='fu'>scDDEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSCDDParams</a></span>(),
<span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>(), <span class='no'>condition</span>, <span class='no'>...</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -208,5 +230,8 @@ simulate. The output is then converted to a SCDDParams object. See
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/scDDSimulate.html b/docs/reference/scDDSimulate.html
index c188de988e69e6344630afec446c4e85e4a06bb6..aa65f8fce98f98b5de6e568eb14995fccbfc4ae3 100644
--- a/docs/reference/scDDSimulate.html
+++ b/docs/reference/scDDSimulate.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="scDD simulation — scDDSimulate" />
+
+<meta property="og:description" content="Simulate counts using the scDD method." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,20 +112,24 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>scDD simulation</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/scDD-simulate.R'><code>R/scDD-simulate.R</code></a></small>
+ <div class="hidden name"><code>scDDSimulate.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Simulate counts using the scDD method.</p>
+ </div>
- <pre class="usage"><span class='fu'>scDDSimulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSCDDParams</a></span>(), <span class='kw'>plots</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>plot.file</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
- <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>(), <span class='no'>...</span>)</pre>
+ <pre class="usage"><span class='fu'>scDDSimulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSCDDParams</a></span>(), <span class='kw'>plots</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+ <span class='kw'>plot.file</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>(), <span class='no'>...</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -196,5 +217,8 @@ single-cell RNA-seq experiments. Genome Biology (2016).</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/setParam.html b/docs/reference/setParam.html
index 25667556cb6f92e6f8c58b279a5fd65f082b515a..c238ca25c5b9b13e93b8854a375f932d1425844f 100644
--- a/docs/reference/setParam.html
+++ b/docs/reference/setParam.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Set a parameter — setParam" />
+
+<meta property="og:description" content="Function for setting parameter values." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,15 +112,19 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Set a parameter</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/AllGenerics.R'><code>R/AllGenerics.R</code></a>, <a href='https://github.com/Oshlack/splatter/blob/master/R/BASiCSParams-methods.R'><code>R/BASiCSParams-methods.R</code></a>, <a href='https://github.com/Oshlack/splatter/blob/master/R/Lun2Params-methods.R'><code>R/Lun2Params-methods.R</code></a>, and 7 more</small>
+ <div class="hidden name"><code>setParam.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Function for setting parameter values.</p>
+ </div>
<pre class="usage"><span class='fu'>setParam</span>(<span class='no'>object</span>, <span class='no'>name</span>, <span class='no'>value</span>)
@@ -131,7 +152,7 @@
<span class='co'># S4 method for ZINBParams</span>
<span class='fu'>setParam</span>(<span class='no'>object</span>, <span class='no'>name</span>, <span class='no'>value</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -160,7 +181,7 @@
#>
#> Global:
#> (GENES) (Cells) [Seed]
-#> 100 100 171612
+#> 100 100 667401
#>
#> 3 additional parameters
#>
@@ -199,5 +220,8 @@
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/setParamUnchecked.html b/docs/reference/setParamUnchecked.html
index eb023a41d84931337a7e8da49074f22604b2ae34..39253e00a8f26475b635a1774a98e2ef781034ba 100644
--- a/docs/reference/setParamUnchecked.html
+++ b/docs/reference/setParamUnchecked.html
@@ -18,13 +18,28 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Set a parameter UNCHECKED — setParamUnchecked" />
+
+<meta property="og:description" content="Function for setting parameter values. THE OUTPUT IS NOT CHECKED FOR
+VALIDITY!" />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +49,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +72,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +87,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +105,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,23 +113,27 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Set a parameter UNCHECKED</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/AllGenerics.R'><code>R/AllGenerics.R</code></a>, <a href='https://github.com/Oshlack/splatter/blob/master/R/Params-methods.R'><code>R/Params-methods.R</code></a></small>
+ <div class="hidden name"><code>setParamUnchecked.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Function for setting parameter values. THE OUTPUT IS NOT CHECKED FOR
VALIDITY!</p>
+ </div>
<pre class="usage"><span class='fu'>setParamUnchecked</span>(<span class='no'>object</span>, <span class='no'>name</span>, <span class='no'>value</span>)
<span class='co'># S4 method for Params</span>
<span class='fu'>setParamUnchecked</span>(<span class='no'>object</span>, <span class='no'>name</span>, <span class='no'>value</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -157,5 +179,8 @@ VALIDITY!</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/setParams.html b/docs/reference/setParams.html
index 9eaa5750b684b6d2a0e0bd00c6bf14fe39e568ac..55aec388f6e6732640c8a8e78b7e3280cba6d8d3 100644
--- a/docs/reference/setParams.html
+++ b/docs/reference/setParams.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Set parameters — setParams" />
+
+<meta property="og:description" content="Set multiple parameters in a Params object." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,19 +112,23 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Set parameters</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/params-functions.R'><code>R/params-functions.R</code></a></small>
+ <div class="hidden name"><code>setParams.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Set multiple parameters in a Params object.</p>
+ </div>
<pre class="usage"><span class='fu'>setParams</span>(<span class='no'>params</span>, <span class='kw'>update</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -146,7 +167,7 @@ them manually), see examples.</p>
#>
#> Global:
#> (Genes) (Cells) [Seed]
-#> 10000 100 171612
+#> 10000 100 667401
#>
#> 3 additional parameters
#>
@@ -164,7 +185,7 @@ them manually), see examples.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 1000 50 171612
+#> 1000 50 667401
#>
#> 3 additional parameters
#>
@@ -182,7 +203,7 @@ them manually), see examples.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 1000 50 171612
+#> 1000 50 667401
#>
#> 3 additional parameters
#>
@@ -222,5 +243,8 @@ them manually), see examples.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/setParamsUnchecked.html b/docs/reference/setParamsUnchecked.html
index 0d7ea93cf90280470ee7d87457327fe90ff3ba9c..44d12b82bc3c4950881445e1564881c713bba0c0 100644
--- a/docs/reference/setParamsUnchecked.html
+++ b/docs/reference/setParamsUnchecked.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Set parameters UNCHECKED — setParamsUnchecked" />
+
+<meta property="og:description" content="Set multiple parameters in a Params object." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,19 +112,23 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Set parameters UNCHECKED</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/params-functions.R'><code>R/params-functions.R</code></a></small>
+ <div class="hidden name"><code>setParamsUnchecked.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Set multiple parameters in a Params object.</p>
+ </div>
<pre class="usage"><span class='fu'>setParamsUnchecked</span>(<span class='no'>params</span>, <span class='kw'>update</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -165,5 +186,8 @@ them manually), see examples. THE FINAL OBJECT IS NOT CHECKED FOR VALIDITY!</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/showDFs.html b/docs/reference/showDFs.html
index f913211b171ef1ad74511347e01fc54c35ae1879..f847334ce6629f8b086378be0dee6cbeaefcaaaf 100644
--- a/docs/reference/showDFs.html
+++ b/docs/reference/showDFs.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Show data.frame — showDFs" />
+
+<meta property="og:description" content="Function used for pretty printing data.frame parameters." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,19 +112,23 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Show data.frame</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/params-functions.R'><code>R/params-functions.R</code></a></small>
+ <div class="hidden name"><code>showDFs.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Function used for pretty printing data.frame parameters.</p>
+ </div>
<pre class="usage"><span class='fu'>showDFs</span>(<span class='no'>dfs</span>, <span class='no'>not.default</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -143,5 +164,8 @@
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/showPP.html b/docs/reference/showPP.html
index 151a11b2f092942dfb59ab8699f94af165cea4f5..33d88d60028bc6fbd0432a75979e2b2c826844fd 100644
--- a/docs/reference/showPP.html
+++ b/docs/reference/showPP.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Show pretty print — showPP" />
+
+<meta property="og:description" content="Function used for pretty printing params object." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,19 +112,23 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Show pretty print</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/params-functions.R'><code>R/params-functions.R</code></a></small>
+ <div class="hidden name"><code>showPP.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Function used for pretty printing params object.</p>
+ </div>
<pre class="usage"><span class='fu'>showPP</span>(<span class='no'>params</span>, <span class='no'>pp</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -149,5 +170,8 @@
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/showValues.html b/docs/reference/showValues.html
index 86c0a1e9f4dfa8073c717290534dd99148d06cfa..cac7b285b98fd7bc8b5a1584c178a8f58d3ef2f7 100644
--- a/docs/reference/showValues.html
+++ b/docs/reference/showValues.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Show vales — showValues" />
+
+<meta property="og:description" content="Function used for pretty printing scale or vector parameters." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,19 +112,23 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Show vales</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/params-functions.R'><code>R/params-functions.R</code></a></small>
+ <div class="hidden name"><code>showValues.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Function used for pretty printing scale or vector parameters.</p>
+ </div>
<pre class="usage"><span class='fu'>showValues</span>(<span class='no'>values</span>, <span class='no'>not.default</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -143,5 +164,8 @@
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/simpleEstimate.html b/docs/reference/simpleEstimate.html
index ea463237ea9c02b0e2c9f15b9153804a0e5d1bf8..9ced2b7f06ba101a450481458917562441deae72 100644
--- a/docs/reference/simpleEstimate.html
+++ b/docs/reference/simpleEstimate.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Estimate simple simulation parameters — simpleEstimate" />
+
+<meta property="og:description" content="Estimate simulation parameters for the simple simulation from a real dataset." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,15 +112,19 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Estimate simple simulation parameters</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/simple-estimate.R'><code>R/simple-estimate.R</code></a></small>
+ <div class="hidden name"><code>simpleEstimate.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Estimate simulation parameters for the simple simulation from a real dataset.</p>
+ </div>
<pre class="usage"><span class='fu'>simpleEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSimpleParams</a></span>())
@@ -114,7 +135,7 @@
<span class='co'># S3 method for matrix</span>
<span class='fu'>simpleEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSimpleParams</a></span>())</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -152,7 +173,7 @@ details on the parameters.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 171612
+#> 2000 40 667401
#>
#> 3 additional parameters
#>
@@ -192,5 +213,8 @@ details on the parameters.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/simpleSimulate.html b/docs/reference/simpleSimulate.html
index cf7047ddfb614ffc48c756324724150a4841c93a..366c133ea5dc92275d84bbb9708bb7e5880b69ab 100644
--- a/docs/reference/simpleSimulate.html
+++ b/docs/reference/simpleSimulate.html
@@ -18,13 +18,28 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Simple simulation — simpleSimulate" />
+
+<meta property="og:description" content="Simulate counts from a simple negative binomial distribution without
+simulated library sizes, differential expression etc." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +49,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +72,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +87,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +105,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,20 +113,24 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Simple simulation</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/simple-simulate.R'><code>R/simple-simulate.R</code></a></small>
+ <div class="hidden name"><code>simpleSimulate.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Simulate counts from a simple negative binomial distribution without
simulated library sizes, differential expression etc.</p>
+ </div>
<pre class="usage"><span class='fu'>simpleSimulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSimpleParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -170,5 +192,8 @@ details of the parameters.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/sparseDCEstimate.html b/docs/reference/sparseDCEstimate.html
index 82b4ad9304e6613ac4a93a153018b26818b32a26..fe37d83eb6e71054ec555e18a50d053c7c171681 100644
--- a/docs/reference/sparseDCEstimate.html
+++ b/docs/reference/sparseDCEstimate.html
@@ -18,13 +18,28 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Estimate SparseDC simulation parameters — sparseDCEstimate" />
+
+<meta property="og:description" content="Estimate simulation parameters for the SparseDC simulation from a real
+dataset." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +49,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +72,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +87,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +105,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,29 +113,33 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Estimate SparseDC simulation parameters</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/sparseDC-estimate.R'><code>R/sparseDC-estimate.R</code></a></small>
+ <div class="hidden name"><code>sparseDCEstimate.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Estimate simulation parameters for the SparseDC simulation from a real
dataset.</p>
+ </div>
<pre class="usage"><span class='fu'>sparseDCEstimate</span>(<span class='no'>counts</span>, <span class='no'>conditions</span>, <span class='no'>nclusters</span>, <span class='kw'>norm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSparseDCParams</a></span>())
<span class='co'># S3 method for SingleCellExperiment</span>
-<span class='fu'>sparseDCEstimate</span>(<span class='no'>counts</span>, <span class='no'>conditions</span>, <span class='no'>nclusters</span>,
- <span class='kw'>norm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSparseDCParams</a></span>())
+<span class='fu'>sparseDCEstimate</span>(<span class='no'>counts</span>, <span class='no'>conditions</span>,
+ <span class='no'>nclusters</span>, <span class='kw'>norm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSparseDCParams</a></span>())
<span class='co'># S3 method for matrix</span>
-<span class='fu'>sparseDCEstimate</span>(<span class='no'>counts</span>, <span class='no'>conditions</span>, <span class='no'>nclusters</span>, <span class='kw'>norm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSparseDCParams</a></span>())</pre>
+<span class='fu'>sparseDCEstimate</span>(<span class='no'>counts</span>, <span class='no'>conditions</span>, <span class='no'>nclusters</span>,
+ <span class='kw'>norm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSparseDCParams</a></span>())</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -174,7 +196,7 @@ input data. The counts are preprocessed using
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 500 20 171612
+#> 500 20 667401
#>
#> 7 additional parameters
#>
@@ -218,5 +240,8 @@ input data. The counts are preprocessed using
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/sparseDCSimulate.html b/docs/reference/sparseDCSimulate.html
index f7ac26d99dd7119300b7dfa3c67fde7323fe5cd7..f71ca37c6e061ff6fefce7ea9a459a9c2f081f67 100644
--- a/docs/reference/sparseDCSimulate.html
+++ b/docs/reference/sparseDCSimulate.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="SparseDC simulation — sparseDCSimulate" />
+
+<meta property="og:description" content="Simulate counts from cluster in two conditions using the SparseDC method." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,19 +112,23 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>SparseDC simulation</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/sparseDC-simulate.R'><code>R/sparseDC-simulate.R</code></a></small>
+ <div class="hidden name"><code>sparseDCSimulate.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Simulate counts from cluster in two conditions using the SparseDC method.</p>
+ </div>
<pre class="usage"><span class='fu'>sparseDCSimulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSparseDCParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -184,5 +205,8 @@ Nucleic Acids Research (2017).</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/splatEstBCV.html b/docs/reference/splatEstBCV.html
index bc5d7fe51f9b2a1fc038ab16d5de62069fee3871..6b3ec33b6adf1e96e8ab5f3890dbb86d9213fe9d 100644
--- a/docs/reference/splatEstBCV.html
+++ b/docs/reference/splatEstBCV.html
@@ -18,13 +18,28 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Estimate Splat Biological Coefficient of Variation parameters — splatEstBCV" />
+
+<meta property="og:description" content="Parameters are estimated using the estimateDisp function
+in the edgeR package." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +49,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +72,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +87,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +105,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,20 +113,24 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Estimate Splat Biological Coefficient of Variation parameters</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/splat-estimate.R'><code>R/splat-estimate.R</code></a></small>
+ <div class="hidden name"><code>splatEstBCV.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Parameters are estimated using the <code><a href='http://www.rdocumentation.org/packages/edgeR/topics/estimateDisp'>estimateDisp</a></code> function
in the <code>edgeR</code> package.</p>
+ </div>
<pre class="usage"><span class='fu'>splatEstBCV</span>(<span class='no'>counts</span>, <span class='no'>params</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -161,5 +183,8 @@ apply a small correction, <code>disp = 0.1 + 0.25 * edgeR.disp</code>.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/splatEstDropout.html b/docs/reference/splatEstDropout.html
index f763342199c29592a1ed2e4f6db4860ac07bb705..772c473f74b6cb472ee65aadf6de28be637cabbb 100644
--- a/docs/reference/splatEstDropout.html
+++ b/docs/reference/splatEstDropout.html
@@ -18,13 +18,28 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Estimate Splat dropout parameters — splatEstDropout" />
+
+<meta property="og:description" content="Estimate the midpoint and shape parameters for the logistic function used
+when simulating dropout." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +49,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +72,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +87,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +105,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,20 +113,24 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Estimate Splat dropout parameters</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/splat-estimate.R'><code>R/splat-estimate.R</code></a></small>
+ <div class="hidden name"><code>splatEstDropout.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Estimate the midpoint and shape parameters for the logistic function used
when simulating dropout.</p>
+ </div>
<pre class="usage"><span class='fu'>splatEstDropout</span>(<span class='no'>norm.counts</span>, <span class='no'>params</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -160,5 +182,8 @@ level dropout is not estimated.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/splatEstLib.html b/docs/reference/splatEstLib.html
index 3fbc04a936f2d18f6c696050468b097930290068..7da2a211bfc7ba006f67c22b630a715ed6357dbf 100644
--- a/docs/reference/splatEstLib.html
+++ b/docs/reference/splatEstLib.html
@@ -18,13 +18,31 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Estimate Splat library size parameters — splatEstLib" />
+
+<meta property="og:description" content="The Shapiro-Wilks test is used to determine if the library sizes are
+normally distributed. If so a normal distribution is fitted to the library
+sizes, if not (most cases) a log-normal distribution is fitted and the
+estimated parameters are added to the params object. See
+fitdist for details on the fitting." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +52,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +75,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +90,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +108,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,23 +116,27 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Estimate Splat library size parameters</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/splat-estimate.R'><code>R/splat-estimate.R</code></a></small>
+ <div class="hidden name"><code>splatEstLib.Rd</code></div>
</div>
+ <div class="ref-description">
- <p>The Shapiro-Wilk test is used to determine if the library sizes are
+ <p>The Shapiro-Wilks test is used to determine if the library sizes are
normally distributed. If so a normal distribution is fitted to the library
sizes, if not (most cases) a log-normal distribution is fitted and the
estimated parameters are added to the params object. See
<code><a href='http://www.rdocumentation.org/packages/fitdistrplus/topics/fitdist'>fitdist</a></code> for details on the fitting.</p>
+ </div>
<pre class="usage"><span class='fu'>splatEstLib</span>(<span class='no'>counts</span>, <span class='no'>params</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -153,5 +178,8 @@ estimated parameters are added to the params object. See
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/splatEstMean.html b/docs/reference/splatEstMean.html
index 91e7ec9bb715aaac9589ade3c12fb1d59c62038e..cad61299ea231e6dda6a281d4e8ce5478ee87c97 100644
--- a/docs/reference/splatEstMean.html
+++ b/docs/reference/splatEstMean.html
@@ -18,13 +18,28 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Estimate Splat mean parameters — splatEstMean" />
+
+<meta property="og:description" content="Estimate rate and shape parameters for the gamma distribution used to
+simulate gene expression means." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +49,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +72,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +87,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +105,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,20 +113,24 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Estimate Splat mean parameters</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/splat-estimate.R'><code>R/splat-estimate.R</code></a></small>
+ <div class="hidden name"><code>splatEstMean.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Estimate rate and shape parameters for the gamma distribution used to
simulate gene expression means.</p>
+ </div>
<pre class="usage"><span class='fu'>splatEstMean</span>(<span class='no'>norm.counts</span>, <span class='no'>params</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -162,5 +184,8 @@ and 90th percentiles.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/splatEstOutlier.html b/docs/reference/splatEstOutlier.html
index c9a7b95af1da084aa758e1587843207c9240b061..feafe8971935af2b17818e237cbc35144de38e15 100644
--- a/docs/reference/splatEstOutlier.html
+++ b/docs/reference/splatEstOutlier.html
@@ -18,13 +18,28 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Estimate Splat expression outlier parameters — splatEstOutlier" />
+
+<meta property="og:description" content="Parameters are estimated by comparing means of individual genes to the
+median mean expression level." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +49,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +72,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +87,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +105,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,20 +113,24 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Estimate Splat expression outlier parameters</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/splat-estimate.R'><code>R/splat-estimate.R</code></a></small>
+ <div class="hidden name"><code>splatEstOutlier.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Parameters are estimated by comparing means of individual genes to the
median mean expression level.</p>
+ </div>
<pre class="usage"><span class='fu'>splatEstOutlier</span>(<span class='no'>norm.counts</span>, <span class='no'>params</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -163,5 +185,8 @@ scale parameters using <code><a href='http://www.rdocumentation.org/packages/fit
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/splatEstimate.html b/docs/reference/splatEstimate.html
index 0d4661afd5a9ff0a04d9d726873780502d5cf7e6..ab01b87b9c45c1a9ecb3f913b37449c12d48393f 100644
--- a/docs/reference/splatEstimate.html
+++ b/docs/reference/splatEstimate.html
@@ -18,13 +18,29 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Estimate Splat simulation parameters — splatEstimate" />
+
+<meta property="og:description" content="Estimate simulation parameters for the Splat simulation from a real
+dataset. See the individual estimation functions for more details on how this
+is done." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +50,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +73,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +88,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +106,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,17 +114,21 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Estimate Splat simulation parameters</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/splat-estimate.R'><code>R/splat-estimate.R</code></a></small>
+ <div class="hidden name"><code>splatEstimate.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Estimate simulation parameters for the Splat simulation from a real
dataset. See the individual estimation functions for more details on how this
is done.</p>
+ </div>
<pre class="usage"><span class='fu'>splatEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSplatParams</a></span>())
@@ -116,7 +139,7 @@ is done.</p>
<span class='co'># S3 method for matrix</span>
<span class='fu'>splatEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSplatParams</a></span>())</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -136,9 +159,9 @@ containing count data to estimate parameters from.</p></td>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
- <p><code><a href='splatEstMean.html'>splatEstMean</a></code>, <code><a href='splatEstLib.html'>splatEstLib</a></code>,
+ <div class='dont-index'><p><code><a href='splatEstMean.html'>splatEstMean</a></code>, <code><a href='splatEstLib.html'>splatEstLib</a></code>,
<code><a href='splatEstOutlier.html'>splatEstOutlier</a></code>, <code><a href='splatEstBCV.html'>splatEstBCV</a></code>,
-<code><a href='splatEstDropout.html'>splatEstDropout</a></code></p>
+<code><a href='splatEstDropout.html'>splatEstDropout</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
@@ -146,12 +169,13 @@ containing count data to estimate parameters from.</p></td>
<span class='fu'>library</span>(<span class='no'>scater</span>)
<span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
-<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>splatEstimate</span>(<span class='no'>sc_example_counts</span>)</div><div class='output co'>#> <span class='message'>NOTE: Library sizes have been found to be normally distributed instead of log-normal. You may want to check this is correct.</span></div><div class='input'><span class='no'>params</span></div><div class='output co'>#> A Params object of class SplatParams
+<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>splatEstimate</span>(<span class='no'>sc_example_counts</span>)
+<span class='no'>params</span></div><div class='output co'>#> A Params object of class SplatParams
#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 171612
+#> 2000 40 667401
#>
#> 28 additional parameters
#>
@@ -164,8 +188,8 @@ containing count data to estimate parameters from.</p></td>
#> 0.0032639148887191 0.419304527025529
#>
#> Library size:
-#> (LOCATION) (SCALE) (NORM)
-#> 388947.775 231618.775891602 TRUE
+#> (LOCATION) (SCALE) (Norm)
+#> 12.7053037408488 0.58910919018286 FALSE
#>
#> Exprs outliers:
#> (PROBABILITY) (LOCATION) (SCALE)
@@ -219,5 +243,8 @@ containing count data to estimate parameters from.</p></td>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/splatSimBCVMeans.html b/docs/reference/splatSimBCVMeans.html
index 5d210d3a8f914b96c50c7f46d07f81c2688de284..328e91bfef28ca7fb15b345d03c6ea8bf3a36602 100644
--- a/docs/reference/splatSimBCVMeans.html
+++ b/docs/reference/splatSimBCVMeans.html
@@ -18,13 +18,29 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Simulate BCV means — splatSimBCVMeans" />
+
+<meta property="og:description" content="Simulate means for each gene in each cell that are adjusted to follow a
+mean-variance trend using Biological Coefficient of Variation taken from
+and inverse gamma distribution." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +50,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +73,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +88,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +106,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,21 +114,25 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Simulate BCV means</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/splat-simulate.R'><code>R/splat-simulate.R</code></a></small>
+ <div class="hidden name"><code>splatSimBCVMeans.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Simulate means for each gene in each cell that are adjusted to follow a
mean-variance trend using Biological Coefficient of Variation taken from
and inverse gamma distribution.</p>
+ </div>
<pre class="usage"><span class='fu'>splatSimBCVMeans</span>(<span class='no'>sim</span>, <span class='no'>params</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -151,5 +174,8 @@ and inverse gamma distribution.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/splatSimBatchCellMeans.html b/docs/reference/splatSimBatchCellMeans.html
index 66a3a1ed4d51078240c62c43138d8e5136b522c4..2dc5f20b39bb28d9bd76a8a19c0a43f62abf4d88 100644
--- a/docs/reference/splatSimBatchCellMeans.html
+++ b/docs/reference/splatSimBatchCellMeans.html
@@ -18,13 +18,28 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Simulate batch means — splatSimBatchCellMeans" />
+
+<meta property="og:description" content="Simulate a mean for each gene in each cell incorporating batch effect
+factors." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +49,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +72,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +87,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +105,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,20 +113,24 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Simulate batch means</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/splat-simulate.R'><code>R/splat-simulate.R</code></a></small>
+ <div class="hidden name"><code>splatSimBatchCellMeans.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Simulate a mean for each gene in each cell incorporating batch effect
factors.</p>
+ </div>
<pre class="usage"><span class='fu'>splatSimBatchCellMeans</span>(<span class='no'>sim</span>, <span class='no'>params</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -150,5 +172,8 @@ factors.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/splatSimBatchEffects.html b/docs/reference/splatSimBatchEffects.html
index 920063de9fc083caf2deb18afcc5c35cba2ae59e..05ed4c5a81e3b4e31db4bf5c85f295d634fcac53 100644
--- a/docs/reference/splatSimBatchEffects.html
+++ b/docs/reference/splatSimBatchEffects.html
@@ -18,13 +18,29 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Simulate batch effects — splatSimBatchEffects" />
+
+<meta property="og:description" content="Simulate batch effects. Batch effect factors for each batch are produced
+using getLNormFactors and these are added along with updated
+means for each batch." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +50,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +73,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +88,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +106,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,21 +114,25 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Simulate batch effects</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/splat-simulate.R'><code>R/splat-simulate.R</code></a></small>
+ <div class="hidden name"><code>splatSimBatchEffects.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Simulate batch effects. Batch effect factors for each batch are produced
using <code><a href='getLNormFactors.html'>getLNormFactors</a></code> and these are added along with updated
means for each batch.</p>
+ </div>
<pre class="usage"><span class='fu'>splatSimBatchEffects</span>(<span class='no'>sim</span>, <span class='no'>params</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -151,5 +174,8 @@ means for each batch.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/splatSimCellMeans.html b/docs/reference/splatSimCellMeans.html
index 522d75dc9bc16659328c3345c45f3e98ec84eac6..f66e44a91a32aa251955ff3f6f6dc2bb5c5c8b31 100644
--- a/docs/reference/splatSimCellMeans.html
+++ b/docs/reference/splatSimCellMeans.html
@@ -18,13 +18,31 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Simulate cell means — splatSimCellMeans" />
+
+<meta property="og:description" content="Simulate a gene by cell matrix giving the mean expression for each gene in
+each cell. Cells start with the mean expression for the group they belong to
+(when simulating groups) or cells are assigned the mean expression from a
+random position on the appropriate path (when simulating paths). The selected
+means are adjusted for each cell's expected library size." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +52,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +75,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +90,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +108,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,12 +116,15 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Simulate cell means</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/splat-simulate.R'><code>R/splat-simulate.R</code></a></small>
+ <div class="hidden name"><code>splatSimCellMeans.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Simulate a gene by cell matrix giving the mean expression for each gene in
each cell. Cells start with the mean expression for the group they belong to
@@ -108,6 +132,7 @@ each cell. Cells start with the mean expression for the group they belong to
random position on the appropriate path (when simulating paths). The selected
means are adjusted for each cell's expected library size.</p>
+ </div>
<pre class="usage"><span class='fu'>splatSimSingleCellMeans</span>(<span class='no'>sim</span>, <span class='no'>params</span>)
@@ -115,7 +140,7 @@ means are adjusted for each cell's expected library size.</p>
<span class='fu'>splatSimPathCellMeans</span>(<span class='no'>sim</span>, <span class='no'>params</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -157,5 +182,8 @@ means are adjusted for each cell's expected library size.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/splatSimDE.html b/docs/reference/splatSimDE.html
index a84b65c1e3a7a9b7e7480fe9a3aa299686ebf356..e394fc9c213b0e743203a7ebc215537f750737a2 100644
--- a/docs/reference/splatSimDE.html
+++ b/docs/reference/splatSimDE.html
@@ -18,13 +18,30 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Simulate group differential expression — splatSimDE" />
+
+<meta property="og:description" content="Simulate differential expression. Differential expression factors for each
+group are produced using getLNormFactors and these are added
+along with updated means for each group. For paths care is taked to make sure
+they are simulated in the correct order." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +51,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +74,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +89,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +107,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,24 +115,28 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Simulate group differential expression</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/splat-simulate.R'><code>R/splat-simulate.R</code></a></small>
+ <div class="hidden name"><code>splatSimDE.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Simulate differential expression. Differential expression factors for each
group are produced using <code><a href='getLNormFactors.html'>getLNormFactors</a></code> and these are added
along with updated means for each group. For paths care is taked to make sure
they are simulated in the correct order.</p>
+ </div>
<pre class="usage"><span class='fu'>splatSimGroupDE</span>(<span class='no'>sim</span>, <span class='no'>params</span>)
<span class='fu'>splatSimPathDE</span>(<span class='no'>sim</span>, <span class='no'>params</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -154,5 +178,8 @@ they are simulated in the correct order.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/splatSimDropout.html b/docs/reference/splatSimDropout.html
index 1387020f260fef1dd3d421b2f2ee86c107d5f3a2..81abab016da0b427f4ee9e9db63424783a078f95 100644
--- a/docs/reference/splatSimDropout.html
+++ b/docs/reference/splatSimDropout.html
@@ -18,13 +18,30 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Simulate dropout — splatSimDropout" />
+
+<meta property="og:description" content="A logistic function is used to form a relationshop between the expression
+level of a gene and the probability of dropout, giving a probability for each
+gene in each cell. These probabilities are used in a Bernoulli distribution
+to decide which counts should be dropped." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +51,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +74,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +89,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +107,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,22 +115,26 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Simulate dropout</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/splat-simulate.R'><code>R/splat-simulate.R</code></a></small>
+ <div class="hidden name"><code>splatSimDropout.Rd</code></div>
</div>
+ <div class="ref-description">
<p>A logistic function is used to form a relationshop between the expression
level of a gene and the probability of dropout, giving a probability for each
gene in each cell. These probabilities are used in a Bernoulli distribution
to decide which counts should be dropped.</p>
+ </div>
<pre class="usage"><span class='fu'>splatSimDropout</span>(<span class='no'>sim</span>, <span class='no'>params</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -152,5 +176,8 @@ to decide which counts should be dropped.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/splatSimGeneMeans.html b/docs/reference/splatSimGeneMeans.html
index f55e7e40a4d11fa8f06b2e6d6b17a39afcb5b1d4..5375508f309a5af51ecff06d235d48875c8c01cc 100644
--- a/docs/reference/splatSimGeneMeans.html
+++ b/docs/reference/splatSimGeneMeans.html
@@ -18,13 +18,29 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Simulate gene means — splatSimGeneMeans" />
+
+<meta property="og:description" content="Simulate gene means from a gamma distribution. Also simulates outlier
+expression factors. Genes with an outlier factor not equal to 1 are replaced
+with the median mean expression multiplied by the outlier factor." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +50,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +73,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +88,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +106,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,21 +114,25 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Simulate gene means</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/splat-simulate.R'><code>R/splat-simulate.R</code></a></small>
+ <div class="hidden name"><code>splatSimGeneMeans.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Simulate gene means from a gamma distribution. Also simulates outlier
expression factors. Genes with an outlier factor not equal to 1 are replaced
with the median mean expression multiplied by the outlier factor.</p>
+ </div>
<pre class="usage"><span class='fu'>splatSimGeneMeans</span>(<span class='no'>sim</span>, <span class='no'>params</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -151,5 +174,8 @@ with the median mean expression multiplied by the outlier factor.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/splatSimLibSizes.html b/docs/reference/splatSimLibSizes.html
index 99a7cb8759960150b6a02a3587168ee16ce799c0..400123fa1865dec2baba6ec8c2268abfd306c566 100644
--- a/docs/reference/splatSimLibSizes.html
+++ b/docs/reference/splatSimLibSizes.html
@@ -18,13 +18,29 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Simulate library sizes — splatSimLibSizes" />
+
+<meta property="og:description" content="Simulate expected library sizes. Typically a log-normal distribution is used
+but there is also the option to use a normal distribution. In this case any
+negative values are set to half the minimum non-zero value." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +50,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +73,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +88,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +106,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,21 +114,25 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Simulate library sizes</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/splat-simulate.R'><code>R/splat-simulate.R</code></a></small>
+ <div class="hidden name"><code>splatSimLibSizes.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Simulate expected library sizes. Typically a log-normal distribution is used
but there is also the option to use a normal distribution. In this case any
negative values are set to half the minimum non-zero value.</p>
+ </div>
<pre class="usage"><span class='fu'>splatSimLibSizes</span>(<span class='no'>sim</span>, <span class='no'>params</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -151,5 +174,8 @@ negative values are set to half the minimum non-zero value.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/splatSimTrueCounts.html b/docs/reference/splatSimTrueCounts.html
index 55f89b76eede5c6d4931265a87f1bd2e81c8d7f3..1c3b745daa4ee725f977ec948bece64289f320b2 100644
--- a/docs/reference/splatSimTrueCounts.html
+++ b/docs/reference/splatSimTrueCounts.html
@@ -18,13 +18,29 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Simulate true counts — splatSimTrueCounts" />
+
+<meta property="og:description" content="Simulate a true counts matrix. Counts are simulated from a poisson
+distribution where Each gene in each cell has it's own mean based on the
+group (or path position), expected library size and BCV." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +50,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +73,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +88,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +106,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,21 +114,25 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Simulate true counts</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/splat-simulate.R'><code>R/splat-simulate.R</code></a></small>
+ <div class="hidden name"><code>splatSimTrueCounts.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Simulate a true counts matrix. Counts are simulated from a poisson
distribution where Each gene in each cell has it's own mean based on the
group (or path position), expected library size and BCV.</p>
+ </div>
<pre class="usage"><span class='fu'>splatSimTrueCounts</span>(<span class='no'>sim</span>, <span class='no'>params</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -151,5 +174,8 @@ group (or path position), expected library size and BCV.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/splatSimulate.html b/docs/reference/splatSimulate.html
index 6cb201b10396df49895e5c52a6408606d34daa87..ae36dcd087ef88a05f08d9cc75ec26dfde751956 100644
--- a/docs/reference/splatSimulate.html
+++ b/docs/reference/splatSimulate.html
@@ -18,13 +18,28 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Splat simulation — splatSimulate" />
+
+<meta property="og:description" content="Simulate count data from a fictional single-cell RNA-seq experiment using
+the Splat method." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +49,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +72,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +87,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +105,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,16 +113,20 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Splat simulation</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/splat-simulate.R'><code>R/splat-simulate.R</code></a></small>
+ <div class="hidden name"><code>splatSimulate.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Simulate count data from a fictional single-cell RNA-seq experiment using
the Splat method.</p>
+ </div>
<pre class="usage"><span class='fu'>splatSimulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSplatParams</a></span>(), <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"single"</span>, <span class='st'>"groups"</span>,
<span class='st'>"paths"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
@@ -115,7 +137,7 @@ the Splat method.</p>
<span class='fu'>splatSimulatePaths</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSplatParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -220,16 +242,16 @@ sequencing data. Genome Biology (2017).</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
- <p><code><a href='splatSimLibSizes.html'>splatSimLibSizes</a></code>, <code><a href='splatSimGeneMeans.html'>splatSimGeneMeans</a></code>,
+ <div class='dont-index'><p><code><a href='splatSimLibSizes.html'>splatSimLibSizes</a></code>, <code><a href='splatSimGeneMeans.html'>splatSimGeneMeans</a></code>,
<code><a href='splatSimBatchEffects.html'>splatSimBatchEffects</a></code>, <code><a href='splatSimBatchCellMeans.html'>splatSimBatchCellMeans</a></code>,
<code><a href='splatSimDE.html'>splatSimDE</a></code>, <code><a href='splatSimCellMeans.html'>splatSimCellMeans</a></code>,
<code><a href='splatSimBCVMeans.html'>splatSimBCVMeans</a></code>, <code><a href='splatSimTrueCounts.html'>splatSimTrueCounts</a></code>,
-<code><a href='splatSimDropout.html'>splatSimDropout</a></code></p>
+<code><a href='splatSimDropout.html'>splatSimDropout</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># Simulation with default parameters</span>
-<span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>splatSimulate</span>()</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts..</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><span class='co'># NOT RUN {</span>
+<span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>splatSimulate</span>()</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><span class='co'># NOT RUN {</span>
<span class='co'># Simulation with different number of genes</span>
<span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>splatSimulate</span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>)
<span class='co'># Simulation with custom parameters</span>
@@ -274,5 +296,8 @@ sequencing data. Genome Biology (2017).</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/splatter.html b/docs/reference/splatter.html
index 63791c0c53f1d21624a1e666b345b47c5d500b54..780d10b216c85c0511b5f8440fd598f93f8ff775 100644
--- a/docs/reference/splatter.html
+++ b/docs/reference/splatter.html
@@ -18,13 +18,28 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="splatter. — splatter" />
+
+<meta property="og:description" content="splatter is a package for the well-documented and reproducible
+simulation of single-cell RNA-seq count data." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +49,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +72,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +87,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +105,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,16 +113,20 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>splatter.</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/splatter-package.R'><code>R/splatter-package.R</code></a></small>
+ <div class="hidden name"><code>splatter.Rd</code></div>
</div>
+ <div class="ref-description">
<p><span class="pkg">splatter</span> is a package for the well-documented and reproducible
simulation of single-cell RNA-seq count data.</p>
+ </div>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
@@ -114,8 +136,8 @@ the estimation of model parameters.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
- <p>Zappia L, Phipson B, Oshlack A. Splatter: Simulation Of Single-Cell RNA
-Sequencing Data. bioRxiv. 2017; doi:10.1101/133173</p>
+ <div class='dont-index'><p>Zappia L, Phipson B, Oshlack A. Splatter: Simulation Of Single-Cell RNA
+Sequencing Data. bioRxiv. 2017; doi:10.1101/133173</p></div>
</div>
@@ -143,5 +165,8 @@ Sequencing Data. bioRxiv. 2017; doi:10.1101/133173</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/summariseDiff.html b/docs/reference/summariseDiff.html
index 51d407f61f082ff762756fc5b760e283fa82aa38..eec87084e1f4c9a97037ba59bc03b27499e153f1 100644
--- a/docs/reference/summariseDiff.html
+++ b/docs/reference/summariseDiff.html
@@ -18,13 +18,29 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Summarise diffSCESs — summariseDiff" />
+
+<meta property="og:description" content="Summarise the results of diffSCEs. Calculates the Median
+Absolute Deviation (MAD), Mean Absolute Error (MAE) and Root Mean Squared
+Error (RMSE) for the various properties and ranks them." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +50,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +73,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +88,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +106,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,21 +114,25 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Summarise diffSCESs</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/compare.R'><code>R/compare.R</code></a></small>
+ <div class="hidden name"><code>summariseDiff.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Summarise the results of <code><a href='diffSCEs.html'>diffSCEs</a></code>. Calculates the Median
Absolute Deviation (MAD), Mean Absolute Error (MAE) and Root Mean Squared
Error (RMSE) for the various properties and ranks them.</p>
+ </div>
<pre class="usage"><span class='fu'>summariseDiff</span>(<span class='no'>diff</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -124,23 +147,23 @@ Error (RMSE) for the various properties and ranks them.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts..</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'><a href='diffSCEs.html'>diffSCEs</a></span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)</div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
+ <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'><a href='diffSCEs.html'>diffSCEs</a></span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)</div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
#> <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
#> <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='input'><span class='no'>summary</span> <span class='kw'><-</span> <span class='fu'>summariseDiff</span>(<span class='no'>difference</span>)
<span class='fu'>head</span>(<span class='no'>summary</span>)</div><div class='output co'>#> Dataset Statistic MAD MADScaled MADRank MAE MAEScaled
-#> 1 Splat Mean 2.617539 NaN 1 2.620761 NaN
-#> 2 Splat Variance 11.320287 NaN 1 10.223665 NaN
-#> 3 Splat ZerosGene 35.000000 NaN 1 41.665000 NaN
-#> 4 Splat MeanVar 10.533179 NaN 1 12.061862 NaN
-#> 5 Splat MeanZeros 45.000000 NaN 1 43.805000 NaN
-#> 6 Splat LibSize 59620.000000 NaN 1 62014.200000 NaN
-#> MAERank RMSE RMSEScaled RMSERank
-#> 1 1 3.164726 NaN 1
-#> 2 1 12.986116 NaN 1
-#> 3 1 45.973090 NaN 1
-#> 4 1 15.097781 NaN 1
-#> 5 1 53.529198 NaN 1
-#> 6 1 63276.140327 NaN 1</div></pre>
+#> 1 Splat Mean 2.623408 NaN 1 2.659195 NaN
+#> 2 Splat Variance 11.848783 NaN 1 10.505147 NaN
+#> 3 Splat ZerosGene 40.000000 NaN 1 44.110000 NaN
+#> 4 Splat MeanVar 11.400920 NaN 1 12.415584 NaN
+#> 5 Splat MeanZeros 45.000000 NaN 1 43.945000 NaN
+#> 6 Splat LibSize 55997.500000 NaN 1 56484.550000 NaN
+#> MAERank RMSE RMSEScaled RMSERank
+#> 1 1 3.21666 NaN 1
+#> 2 1 13.21816 NaN 1
+#> 3 1 47.71111 NaN 1
+#> 4 1 15.39405 NaN 1
+#> 5 1 53.33878 NaN 1
+#> 6 1 57530.14610 NaN 1</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -167,5 +190,8 @@ Error (RMSE) for the various properties and ranks them.</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/winsorize.html b/docs/reference/winsorize.html
index f5a1067dbf341aa2441f19d44b396f44ed2a5752..ad3548cb5e3d7f4613be0539de95c4acf7846208 100644
--- a/docs/reference/winsorize.html
+++ b/docs/reference/winsorize.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Winsorize vector — winsorize" />
+
+<meta property="og:description" content="Set outliers in a numeric vector to a specified percentile." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,19 +112,23 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Winsorize vector</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/utils.R'><code>R/utils.R</code></a></small>
+ <div class="hidden name"><code>winsorize.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Set outliers in a numeric vector to a specified percentile.</p>
+ </div>
<pre class="usage"><span class='fu'>winsorize</span>(<span class='no'>x</span>, <span class='no'>q</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -149,5 +170,8 @@
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/zinbEstimate.html b/docs/reference/zinbEstimate.html
index 11899967327bb0e7c5a1320a63a31e36b3f067d9..47f4a54d1e446d936938e8183452bc370d07e286 100644
--- a/docs/reference/zinbEstimate.html
+++ b/docs/reference/zinbEstimate.html
@@ -18,13 +18,28 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Estimate ZINB-WaVE simulation parameters — zinbEstimate" />
+
+<meta property="og:description" content="Estimate simulation parameters for the ZINB-WaVE simulation from a real
+dataset." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +49,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +72,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +87,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +105,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,34 +113,40 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Estimate ZINB-WaVE simulation parameters</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/zinb-estimate.R'><code>R/zinb-estimate.R</code></a></small>
+ <div class="hidden name"><code>zinbEstimate.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Estimate simulation parameters for the ZINB-WaVE simulation from a real
dataset.</p>
+ </div>
<pre class="usage"><span class='fu'>zinbEstimate</span>(<span class='no'>counts</span>, <span class='kw'>design.samples</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>design.genes</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
- <span class='kw'>common.disp</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>iter.init</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>iter.opt</span> <span class='kw'>=</span> <span class='fl'>25</span>, <span class='kw'>stop.opt</span> <span class='kw'>=</span> <span class='fl'>1e-04</span>,
- <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newZINBParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>(), <span class='no'>...</span>)
-
-<span class='co'># S3 method for SingleCellExperiment</span>
-<span class='fu'>zinbEstimate</span>(<span class='no'>counts</span>, <span class='kw'>design.samples</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
- <span class='kw'>design.genes</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>common.disp</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>iter.init</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>iter.opt</span> <span class='kw'>=</span> <span class='fl'>25</span>,
+ <span class='kw'>common.disp</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>iter.init</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>iter.opt</span> <span class='kw'>=</span> <span class='fl'>25</span>,
<span class='kw'>stop.opt</span> <span class='kw'>=</span> <span class='fl'>1e-04</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newZINBParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>(), <span class='no'>...</span>)
+<span class='co'># S3 method for SingleCellExperiment</span>
+<span class='fu'>zinbEstimate</span>(<span class='no'>counts</span>,
+ <span class='kw'>design.samples</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>design.genes</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>common.disp</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+ <span class='kw'>iter.init</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>iter.opt</span> <span class='kw'>=</span> <span class='fl'>25</span>, <span class='kw'>stop.opt</span> <span class='kw'>=</span> <span class='fl'>1e-04</span>,
+ <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newZINBParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>(),
+ <span class='no'>...</span>)
+
<span class='co'># S3 method for matrix</span>
<span class='fu'>zinbEstimate</span>(<span class='no'>counts</span>, <span class='kw'>design.samples</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
- <span class='kw'>design.genes</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>common.disp</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>iter.init</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>iter.opt</span> <span class='kw'>=</span> <span class='fl'>25</span>,
- <span class='kw'>stop.opt</span> <span class='kw'>=</span> <span class='fl'>1e-04</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newZINBParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>(), <span class='no'>...</span>)</pre>
+ <span class='kw'>design.genes</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>common.disp</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>iter.init</span> <span class='kw'>=</span> <span class='fl'>2</span>,
+ <span class='kw'>iter.opt</span> <span class='kw'>=</span> <span class='fl'>25</span>, <span class='kw'>stop.opt</span> <span class='kw'>=</span> <span class='fl'>1e-04</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newZINBParams</a></span>(),
+ <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>(), <span class='no'>...</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -224,5 +248,8 @@ the fitted model and inserts it into a <code><a href='ZINBParams.html'>ZINBParam
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/zinbSimulate.html b/docs/reference/zinbSimulate.html
index bfd11132c438b8bf747cead2c4ab3e9c23c04300..f75ed36cbf8daef9071b29d9580ac2c0dddddb62 100644
--- a/docs/reference/zinbSimulate.html
+++ b/docs/reference/zinbSimulate.html
@@ -18,13 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+
<link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="ZINB-WaVE simulation — zinbSimulate" />
+
+<meta property="og:description" content="Simulate counts using the ZINB-WaVE method." />
+<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -34,16 +48,14 @@
<![endif]-->
-<!-- Google analytics -->
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
<script>
- (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
- (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
- m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
- })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-
- ga('create', 'UA-52309538-4', 'auto');
- ga('send', 'pageview');
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+ gtag('config', 'UA-52309538-4');
</script>
</head>
@@ -59,8 +71,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">splatter</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -70,13 +86,13 @@
</a>
</li>
<li>
- <a href="../articles/splatter.html">Get Started</a>
+ <a href="../articles/splatter.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../news/index.html">News</a>
+ <a href="../news/index.html">Changelog</a>
</li>
</ul>
@@ -88,6 +104,7 @@
</a>
</li>
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -95,19 +112,23 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>ZINB-WaVE simulation</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/zinb-simulate.R'><code>R/zinb-simulate.R</code></a></small>
+ <div class="hidden name"><code>zinbSimulate.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Simulate counts using the ZINB-WaVE method.</p>
+ </div>
<pre class="usage"><span class='fu'>zinbSimulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newZINBParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -182,5 +203,8 @@ bioRxiv (2017).</p>
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
new file mode 100644
index 0000000000000000000000000000000000000000..aa9d8d203d73e2543e4af1799371052490904b10
--- /dev/null
+++ b/docs/sitemap.xml
@@ -0,0 +1,225 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
+ <url>
+ <loc>http://oshlack.github.io/splatter/index.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/BASiCSEstimate.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/BASiCSParams.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/BASiCSSimulate.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/Lun2Params.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/LunParams.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/MFAParams.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/Params.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/PhenoParams.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/SCDDParams.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/SimpleParams.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/SparseDCParams.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/SplatParams.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/ZINBParams.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/addFeatureStats.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/addGeneLengths.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/bridge.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/compareSCEs.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/diffSCEs.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/expandParams.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/getLNormFactors.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/getParam.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/getParams.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/getPathOrder.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/listSims.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/logistic.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/lun2Estimate.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/lun2Simulate.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/lunEstimate.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/lunSimulate.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/makeCompPanel.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/makeDiffPanel.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/makeOverallPanel.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/mfaEstimate.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/mfaSimulate.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/newParams.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/phenoEstimate.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/phenoSimulate.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/rbindMatched.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/scDDEstimate.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/scDDSimulate.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/setParam.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/setParamUnchecked.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/setParams.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/setParamsUnchecked.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/showDFs.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/showPP.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/showValues.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/simpleEstimate.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/simpleSimulate.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/sparseDCEstimate.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/sparseDCSimulate.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/splatEstBCV.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/splatEstDropout.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/splatEstLib.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/splatEstMean.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/splatEstOutlier.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/splatEstimate.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/splatSimBCVMeans.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/splatSimBatchCellMeans.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/splatSimBatchEffects.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/splatSimCellMeans.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/splatSimDE.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/splatSimDropout.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/splatSimGeneMeans.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/splatSimLibSizes.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/splatSimTrueCounts.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/splatSimulate.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/splatter.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/summariseDiff.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/winsorize.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/zinbEstimate.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/zinbSimulate.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/articles/splatter.html</loc>
+ </url>
+</urlset>
diff --git a/index.md b/index.md
index 90cfdc6369d87c00d275d3d441b1f04cbca521f9..b6419effa352d13587d7ce0a7bb6e69d950d6d1e 100644
--- a/index.md
+++ b/index.md
@@ -30,18 +30,18 @@ https://bioconductor.org/packages/splatter.
Splatter has been accepted into the latest version of [Bioconductor][bioc]
and hence requires the latest version of R (>=3.4).
-If you have these installed Splatter can be installed from Bioconductor using
-`biocLite`:
+It can be installed from Bioconductor with:
```{r}
-source("https://bioconductor.org/biocLite.R")
-biocLite("splatter")
+if (!requireNamespace("BiocManager", quietly=TRUE))
+ install.packages("BiocManager")
+BiocManager::install("splatter")
```
If you wish to build a local version of the vignette use:
```{r}
-biocLite("splatter", build_vignettes=TRUE)
+BiocManager::install("splatter", build_vignettes=TRUE)
```
This will also build the vignette and install all suggested dependencies (which
@@ -55,11 +55,10 @@ If you want to try the [development version][devel] this can also be installed
from Bioconductor:
```{r}
-library(BiocInstaller)
-useDevel()
-biocValid() # checks for out of date packages
-biocLite() # (optional) updates out of date packages
-biocLite("splatter")
+library(BiocManager)
+valid() # checks for out of date packages
+BiocManager::install() # (optional) updates out of date packages
+BiocManager::install("splatter")
```
Depending on the current release cycle you may also need to install the
diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
index 4c7cd3bc2283ca639a23d166a8c4eeba3f6fb364..b43862c6092f087996a77f7134806fe2df05ec25 100644
--- a/inst/NEWS.Rd
+++ b/inst/NEWS.Rd
@@ -1,7 +1,17 @@
\name{NEWS}
\title{News for Package \pkg{splatter}}
-\section{Version 1.3.5, Bioconductor 3.7 Release (2017-04-25)}{
+\section{Version 1.6.0, Bioconductor 3.8 Release (2018-10-29)}{
+ \itemize{
+ \item{Fix bug and improve normality testing in splatEstLib}
+ \item{Fixes for compatibility with the latest version of BASiCS,
+ BASiCSEstimate now uses the regression method}
+ \item{Fix bug in getLNormFactors when reversing factors less than one}
+ \item{Various updates to tests and documentation}
+ }
+}
+
+\section{Version 1.3.5, Bioconductor 3.7 Release (2018-04-25)}{
\itemize{
\item{Move scater to Imports and add scater version}
\item{Remove lingering references to SCESets}
diff --git a/man/BASiCSEstimate.Rd b/man/BASiCSEstimate.Rd
index aa9c6a3109041c691695b1b079ad914c7953c2d3..b7d28f782a8c97c1c79b5f2b22ad5d608a518f59 100644
--- a/man/BASiCSEstimate.Rd
+++ b/man/BASiCSEstimate.Rd
@@ -7,16 +7,18 @@
\title{Estimate BASiCS simulation parameters}
\usage{
BASiCSEstimate(counts, spike.info = NULL, batch = NULL, n = 20000,
- thin = 10, burn = 5000, params = newBASiCSParams(), verbose = TRUE,
- progress = TRUE, ...)
+ thin = 10, burn = 5000, regression = TRUE,
+ params = newBASiCSParams(), verbose = TRUE, progress = TRUE, ...)
\method{BASiCSEstimate}{SingleCellExperiment}(counts, spike.info = NULL,
batch = NULL, n = 20000, thin = 10, burn = 5000,
- params = newBASiCSParams(), verbose = TRUE, progress = TRUE, ...)
+ regression = TRUE, params = newBASiCSParams(), verbose = TRUE,
+ progress = TRUE, ...)
-\method{BASiCSEstimate}{matrix}(counts, spike.info = NULL, batch = NULL,
- n = 20000, thin = 10, burn = 5000, params = newBASiCSParams(),
- verbose = TRUE, progress = TRUE, ...)
+\method{BASiCSEstimate}{matrix}(counts, spike.info = NULL,
+ batch = NULL, n = 20000, thin = 10, burn = 5000,
+ regression = TRUE, params = newBASiCSParams(), verbose = TRUE,
+ progress = TRUE, ...)
}
\arguments{
\item{counts}{either a counts matrix or a SingleCellExperiment object
@@ -37,6 +39,9 @@ a multiple of \code{thin}.}
\item{burn}{burn-in period for the MCMC sampler. Must be in the range
\code{1 <= burn < n} and a multiple of \code{thin}.}
+\item{regression}{logical. Whether to use regression to identify
+over-dispersion. See \code{\link[BASiCS]{BASiCS_MCMC}} for details.}
+
\item{params}{BASiCSParams object to store estimated values in.}
\item{verbose}{logical. Whether to print progress messages.}
@@ -68,7 +73,7 @@ data("sc_example_counts")
spike.info <- data.frame(Name = rownames(sc_example_counts)[1:10],
Input = rnorm(10, 500, 200),
stringsAsFactors = FALSE)
-params <- BASiCSEstimate(sc_example_counts[1:50, 1:20],
+params <- BASiCSEstimate(sc_example_counts[1:100, 1:30],
spike.info)
params
}
diff --git a/man/addFeatureStats.Rd b/man/addFeatureStats.Rd
index d538fd011e0dcb57590a8f1558f5a492cf3df5e7..2ac4f6ed52da0918568d29b0182a21694394f6b2 100644
--- a/man/addFeatureStats.Rd
+++ b/man/addFeatureStats.Rd
@@ -4,8 +4,8 @@
\alias{addFeatureStats}
\title{Add feature statistics}
\usage{
-addFeatureStats(sce, value = c("counts", "cpm", "tpm", "fpkm"), log = FALSE,
- offset = 1, no.zeros = FALSE)
+addFeatureStats(sce, value = c("counts", "cpm", "tpm", "fpkm"),
+ log = FALSE, offset = 1, no.zeros = FALSE)
}
\arguments{
\item{sce}{SingleCellExperiment to add feature statistics to.}
diff --git a/man/lun2Simulate.Rd b/man/lun2Simulate.Rd
index 4b6c66dfc317aed96b34d707b7b593f93a7e317c..df77ac55ec57956a28bf8b8cb8571087cca5511c 100644
--- a/man/lun2Simulate.Rd
+++ b/man/lun2Simulate.Rd
@@ -4,7 +4,8 @@
\alias{lun2Simulate}
\title{Lun2 simulation}
\usage{
-lun2Simulate(params = newLun2Params(), zinb = FALSE, verbose = TRUE, ...)
+lun2Simulate(params = newLun2Params(), zinb = FALSE, verbose = TRUE,
+ ...)
}
\arguments{
\item{params}{Lun2Params object containing simulation parameters.}
diff --git a/man/lunEstimate.Rd b/man/lunEstimate.Rd
index 63bd4f66b0acd9470701fa4e230c27e1cbcbf98c..207fd60a778f4697adab651973f5f7c798045aeb 100644
--- a/man/lunEstimate.Rd
+++ b/man/lunEstimate.Rd
@@ -8,7 +8,8 @@
\usage{
lunEstimate(counts, params = newLunParams())
-\method{lunEstimate}{SingleCellExperiment}(counts, params = newLunParams())
+\method{lunEstimate}{SingleCellExperiment}(counts,
+ params = newLunParams())
\method{lunEstimate}{matrix}(counts, params = newLunParams())
}
diff --git a/man/makeCompPanel.Rd b/man/makeCompPanel.Rd
index c91b324ee605b9e6ba6c0fa1acb0074efddfa7bc..d9ec714e6bf85f3340582ac054b63e03f9ea667b 100644
--- a/man/makeCompPanel.Rd
+++ b/man/makeCompPanel.Rd
@@ -4,9 +4,9 @@
\alias{makeCompPanel}
\title{Make comparison panel}
\usage{
-makeCompPanel(comp, title = "Comparison", labels = c("Means", "Variance",
- "Mean-variance relationship", "Library size", "Zeros per gene",
- "Zeros per cell", "Mean-zeros relationship"))
+makeCompPanel(comp, title = "Comparison", labels = c("Means",
+ "Variance", "Mean-variance relationship", "Library size",
+ "Zeros per gene", "Zeros per cell", "Mean-zeros relationship"))
}
\arguments{
\item{comp}{list returned by \code{\link{compareSCEs}}.}
diff --git a/man/makeDiffPanel.Rd b/man/makeDiffPanel.Rd
index a0239a85c84d5cd3d04f9c3722b2cb26acaab069..4d772febf14294c50048428c5ef6784a78ed107a 100644
--- a/man/makeDiffPanel.Rd
+++ b/man/makeDiffPanel.Rd
@@ -4,9 +4,10 @@
\alias{makeDiffPanel}
\title{Make difference panel}
\usage{
-makeDiffPanel(diff, title = "Difference comparison", labels = c("Means",
- "Variance", "Library size", "Zeros per cell", "Zeros per gene",
- "Mean-variance relationship", "Mean-zeros relationship"))
+makeDiffPanel(diff, title = "Difference comparison",
+ labels = c("Means", "Variance", "Library size", "Zeros per cell",
+ "Zeros per gene", "Mean-variance relationship",
+ "Mean-zeros relationship"))
}
\arguments{
\item{diff}{list returned by \code{\link{diffSCEs}}.}
diff --git a/man/mfaEstimate.Rd b/man/mfaEstimate.Rd
index ac81d6a541893ffd4d6d7c4f1de585e6dc8300ab..c8ad13e6cf8ff7775d21c36ae89b991470df3b40 100644
--- a/man/mfaEstimate.Rd
+++ b/man/mfaEstimate.Rd
@@ -8,7 +8,8 @@
\usage{
mfaEstimate(counts, params = newMFAParams())
-\method{mfaEstimate}{SingleCellExperiment}(counts, params = newMFAParams())
+\method{mfaEstimate}{SingleCellExperiment}(counts,
+ params = newMFAParams())
\method{mfaEstimate}{matrix}(counts, params = newMFAParams())
}
diff --git a/man/scDDEstimate.Rd b/man/scDDEstimate.Rd
index d5ae4e28c1fa02972b0c920e9a42ba8ed87b0d69..9f15d6d8bd91b933c6e7531f70e222938629c98d 100644
--- a/man/scDDEstimate.Rd
+++ b/man/scDDEstimate.Rd
@@ -13,8 +13,9 @@ scDDEstimate(counts, params = newSCDDParams(), verbose = TRUE,
\method{scDDEstimate}{matrix}(counts, params = newSCDDParams(),
verbose = TRUE, BPPARAM = SerialParam(), conditions, ...)
-\method{scDDEstimate}{SingleCellExperiment}(counts, params = newSCDDParams(),
- verbose = TRUE, BPPARAM = SerialParam(), condition = "condition", ...)
+\method{scDDEstimate}{SingleCellExperiment}(counts,
+ params = newSCDDParams(), verbose = TRUE, BPPARAM = SerialParam(),
+ condition = "condition", ...)
\method{scDDEstimate}{default}(counts, params = newSCDDParams(),
verbose = TRUE, BPPARAM = SerialParam(), condition, ...)
diff --git a/man/scDDSimulate.Rd b/man/scDDSimulate.Rd
index bb7bef373ac716d35c2cf5f6d9b8ae409d3266ea..73916f358be7edd6bde7b0565ab5e6df7b2450bf 100644
--- a/man/scDDSimulate.Rd
+++ b/man/scDDSimulate.Rd
@@ -4,8 +4,8 @@
\alias{scDDSimulate}
\title{scDD simulation}
\usage{
-scDDSimulate(params = newSCDDParams(), plots = FALSE, plot.file = NULL,
- verbose = TRUE, BPPARAM = SerialParam(), ...)
+scDDSimulate(params = newSCDDParams(), plots = FALSE,
+ plot.file = NULL, verbose = TRUE, BPPARAM = SerialParam(), ...)
}
\arguments{
\item{params}{SCDDParams object containing simulation parameters.}
diff --git a/man/sparseDCEstimate.Rd b/man/sparseDCEstimate.Rd
index 4d19581d40821da96be2b7d5d750e24b9bdf0cfd..c9abf4fb5c2318220fef6b2050d54e8486073227 100644
--- a/man/sparseDCEstimate.Rd
+++ b/man/sparseDCEstimate.Rd
@@ -9,11 +9,11 @@
sparseDCEstimate(counts, conditions, nclusters, norm = TRUE,
params = newSparseDCParams())
-\method{sparseDCEstimate}{SingleCellExperiment}(counts, conditions, nclusters,
- norm = TRUE, params = newSparseDCParams())
+\method{sparseDCEstimate}{SingleCellExperiment}(counts, conditions,
+ nclusters, norm = TRUE, params = newSparseDCParams())
-\method{sparseDCEstimate}{matrix}(counts, conditions, nclusters, norm = TRUE,
- params = newSparseDCParams())
+\method{sparseDCEstimate}{matrix}(counts, conditions, nclusters,
+ norm = TRUE, params = newSparseDCParams())
}
\arguments{
\item{counts}{either a counts matrix or an SingleCellExperiment object
diff --git a/man/splatEstLib.Rd b/man/splatEstLib.Rd
index c7eda133a333ffcc2ff1d4df99226919e650c7af..30df262739e3b918071748c8198b1f62f7f20e82 100644
--- a/man/splatEstLib.Rd
+++ b/man/splatEstLib.Rd
@@ -15,7 +15,7 @@ splatEstLib(counts, params)
splatParams object with estimated values.
}
\description{
-The Shapiro-Wilk test is used to determine if the library sizes are
+The Shapiro-Wilks test is used to determine if the library sizes are
normally distributed. If so a normal distribution is fitted to the library
sizes, if not (most cases) a log-normal distribution is fitted and the
estimated parameters are added to the params object. See
diff --git a/man/zinbEstimate.Rd b/man/zinbEstimate.Rd
index cd570beee85d8cbc15f9c03d3dc2eb388df41a6e..5c854a4c252594b067af178e675d697056f3ce06 100644
--- a/man/zinbEstimate.Rd
+++ b/man/zinbEstimate.Rd
@@ -7,18 +7,20 @@
\title{Estimate ZINB-WaVE simulation parameters}
\usage{
zinbEstimate(counts, design.samples = NULL, design.genes = NULL,
- common.disp = TRUE, iter.init = 2, iter.opt = 25, stop.opt = 1e-04,
- params = newZINBParams(), verbose = TRUE, BPPARAM = SerialParam(), ...)
-
-\method{zinbEstimate}{SingleCellExperiment}(counts, design.samples = NULL,
- design.genes = NULL, common.disp = TRUE, iter.init = 2, iter.opt = 25,
+ common.disp = TRUE, iter.init = 2, iter.opt = 25,
stop.opt = 1e-04, params = newZINBParams(), verbose = TRUE,
BPPARAM = SerialParam(), ...)
+\method{zinbEstimate}{SingleCellExperiment}(counts,
+ design.samples = NULL, design.genes = NULL, common.disp = TRUE,
+ iter.init = 2, iter.opt = 25, stop.opt = 1e-04,
+ params = newZINBParams(), verbose = TRUE, BPPARAM = SerialParam(),
+ ...)
+
\method{zinbEstimate}{matrix}(counts, design.samples = NULL,
- design.genes = NULL, common.disp = TRUE, iter.init = 2, iter.opt = 25,
- stop.opt = 1e-04, params = newZINBParams(), verbose = TRUE,
- BPPARAM = SerialParam(), ...)
+ design.genes = NULL, common.disp = TRUE, iter.init = 2,
+ iter.opt = 25, stop.opt = 1e-04, params = newZINBParams(),
+ verbose = TRUE, BPPARAM = SerialParam(), ...)
}
\arguments{
\item{counts}{either a counts matrix or a SingleCellExperiment object
diff --git a/tests/testthat/test-BASiCS-simulate.R b/tests/testthat/test-BASiCS-simulate.R
new file mode 100644
index 0000000000000000000000000000000000000000..98d6cade8d45e99a33f0b9c99891bae84cffd483
--- /dev/null
+++ b/tests/testthat/test-BASiCS-simulate.R
@@ -0,0 +1,6 @@
+context("BASiCS simulation")
+
+test_that("BASiCS simulation output is valid", {
+ skip_if_not_installed("BASiCS")
+ expect_true(validObject(sparseDCSimulate()))
+})
diff --git a/tests/testthat/test-BASiCSEstimate.R b/tests/testthat/test-BASiCSEstimate.R
new file mode 100644
index 0000000000000000000000000000000000000000..3e1df27accc507d6fbd9a58cfe8b85b26a7d33a6
--- /dev/null
+++ b/tests/testthat/test-BASiCSEstimate.R
@@ -0,0 +1,28 @@
+context("BASiCSEstimate")
+
+library(scater)
+data("sc_example_counts")
+
+test_that("BASiCSEstimate works", {
+ skip_if_not_installed("BASiCS")
+ set.seed(1)
+ spike.info <- data.frame(Name = rownames(sc_example_counts)[1:10],
+ Input = rnorm(10, 500, 200),
+ stringsAsFactors = FALSE)
+ counts <- sc_example_counts[, 1:30]
+ counts <- counts[rowSums(counts) != 0, ]
+ params <- BASiCSEstimate(counts[1:100, ],
+ spike.info, verbose = FALSE, progress = FALSE)
+ expect_true(validObject(params))
+})
+
+test_that("BASiCSEstimate works without spikes", {
+ skip_if_not_installed("BASiCS")
+ set.seed(1)
+ counts <- sc_example_counts[, 1:30]
+ counts <- counts[rowSums(counts) != 0, ]
+ batch <- sample(1:2, ncol(counts), replace = TRUE)
+ params <- BASiCSEstimate(counts[1:100, ], batch = batch,
+ verbose = FALSE, progress = FALSE)
+ expect_true(validObject(params))
+})
diff --git a/tests/testthat/test-BASiCSParams.R b/tests/testthat/test-BASiCSParams.R
index 97866e7e63fe6bbae2d8994faf9764526f806687..fc9f8b79b2140f1309955fd86917caf31e886861 100644
--- a/tests/testthat/test-BASiCSParams.R
+++ b/tests/testthat/test-BASiCSParams.R
@@ -1,12 +1,16 @@
context("BASiCSParams")
-params <- newBASiCSParams()
+if (requireNamespace("BASiCS", quietly = TRUE)) {
+ params <- newBASiCSParams()
+}
test_that("printing works", {
+ skip_if_not_installed("BASiCS")
expect_output(show(params), "A Params object of class BASiCSParams")
})
test_that("gene.params checks work", {
+ skip_if_not_installed("BASiCS")
expect_error(setParam(params, "gene.params", data.frame(A = 1, B = 1)),
"gene.params: Incorrect column names")
expect_error(setParam(params, "gene.params",
@@ -15,6 +19,7 @@ test_that("gene.params checks work", {
})
test_that("cell.params checks work", {
+ skip_if_not_installed("BASiCS")
expect_error(setParam(params, "cell.params", data.frame(A = 1, B = 1)),
"cell.params: Incorrect column names")
expect_error(setParam(params, "cell.params",
@@ -23,6 +28,7 @@ test_that("cell.params checks work", {
})
test_that("nBatches checks work", {
+ skip_if_not_installed("BASiCS")
expect_error(setParam(params, "nCells", 1),
"nCells cannot be set directly, set batchCells instead")
expect_error(setParam(params, "nBatches", 1),
@@ -30,6 +36,7 @@ test_that("nBatches checks work", {
})
test_that("batchCells checks work", {
+ skip_if_not_installed("BASiCS")
pp <- setParam(params, "batchCells", c(10, 10))
expect_equal(getParam(pp, "nCells"), 20)
expect_equal(getParam(pp, "nBatches"), 2)
diff --git a/tests/testthat/test-MFAEstimate.R b/tests/testthat/test-MFAEstimate.R
index 12cee5cc796b64d179c173e2f1b5583f2fb52edb..ab703c70f0e294c9ee079447acfd6bd7eed927ef 100644
--- a/tests/testthat/test-MFAEstimate.R
+++ b/tests/testthat/test-MFAEstimate.R
@@ -4,6 +4,7 @@ library(scater)
data("sc_example_counts")
test_that("MFAEstimate works", {
+ skip_if_not_installed("mfa")
params <- mfaEstimate(sc_example_counts)
expect_true(validObject(params))
})
diff --git a/tests/testthat/test-MFAParams.R b/tests/testthat/test-MFAParams.R
index 1cd9c19990ff0e3bf06c2c30532f23d828662738..f845b5e6525b2d8a82398e05e3d42c961fd4c4aa 100644
--- a/tests/testthat/test-MFAParams.R
+++ b/tests/testthat/test-MFAParams.R
@@ -1,7 +1,7 @@
context("MFAParams")
-params <- newMFAParams()
-
test_that("printing works", {
+ skip_if_not_installed("mfa")
+ params <- newMFAParams()
expect_output(show(params), "A Params object of class MFAParams")
})
diff --git a/tests/testthat/test-PhenoParams.R b/tests/testthat/test-PhenoParams.R
index d806e99a73ea7b757954fdc0b56989e5ced38297..c6fdbdf5ec2b13c8e92e74c4d66a0492d0a1502c 100644
--- a/tests/testthat/test-PhenoParams.R
+++ b/tests/testthat/test-PhenoParams.R
@@ -1,16 +1,21 @@
context("PhenoParams")
-params <- newPhenoParams()
+if (requireNamespace("phenopath", quietly = TRUE)) {
+ params <- newPhenoParams()
+}
test_that("constructor is valid", {
+ skip_if_not_installed("phenopath")
expect_true(validObject(params))
})
test_that("printing works", {
+ skip_if_not_installed("phenopath")
expect_output(show(params), "A Params object of class PhenoParams")
})
test_that("nGenes checks work", {
+ skip_if_not_installed("phenopath")
expect_error(setParam(params, "nGenes", 1),
"nGenes cannot be set directly")
pp <- setParam(params, "n.de", 0)
diff --git a/tests/testthat/test-SCDDParams.R b/tests/testthat/test-SCDDParams.R
index 05ff5ef034d478516785e809e9d4edae650fca9d..a9895d58edf1bb4ceccb5acbd70d75b9ca1e3619 100644
--- a/tests/testthat/test-SCDDParams.R
+++ b/tests/testthat/test-SCDDParams.R
@@ -1,16 +1,21 @@
context("SCDDParams")
-params <- newSCDDParams()
+if (requireNamespace("scDD", quietly = TRUE)) {
+ params <- newSCDDParams()
+}
test_that("constructor is valid", {
+ skip_if_not_installed("scDD")
expect_true(validObject(params))
})
test_that("printing works", {
+ skip_if_not_installed("scDD")
expect_output(show(params), "A Params object of class SCDDParams")
})
test_that("nGenes checks work", {
+ skip_if_not_installed("scDD")
expect_error(setParam(params, "nGenes", 1),
paste("nGenes cannot be set directly, set nDE, nDP, nDM, nDB,",
"nEE or nEP instead"))
diff --git a/tests/testthat/test-SparseDCParams.R b/tests/testthat/test-SparseDCParams.R
index 642ec927687d26fb6f47428733b2ac5701e308a7..f3714f3dbd20c259d58322a3da5f69965e3a89c9 100644
--- a/tests/testthat/test-SparseDCParams.R
+++ b/tests/testthat/test-SparseDCParams.R
@@ -1,16 +1,21 @@
context("SparseDCParams")
-params <- newSparseDCParams()
+if (requireNamespace("SparseDC", quietly = TRUE)) {
+ params <- newSparseDCParams()
+}
test_that("constructor is valid", {
+ skip_if_not_installed("SparseDC")
expect_true(validObject(params))
})
test_that("printing works", {
+ skip_if_not_installed("SparseDC")
expect_output(show(params), "A Params object of class SparseDCParams")
})
test_that("clusts checks work", {
+ skip_if_not_installed("SparseDC")
expect_error(setParam(params, "clusts.c1", 2),
"is length 1 it must equal 1")
expect_error(setParam(params, "clusts.c2", 2),
diff --git a/tests/testthat/test-ZINBParams.R b/tests/testthat/test-ZINBParams.R
index 061bb8ae7675db988e532f112cdf24cf4dea822a..1d30a3ac3892010f66943452d2ab9840f1998ecd 100644
--- a/tests/testthat/test-ZINBParams.R
+++ b/tests/testthat/test-ZINBParams.R
@@ -1,16 +1,21 @@
context("ZINBParams")
-params <- newZINBParams()
+if (requireNamespace("zinbwave", quietly = TRUE)) {
+ params <- newZINBParams()
+}
test_that("constructor is valid", {
+ skip_if_not_installed("zinbwave")
expect_true(validObject(params))
})
test_that("printing works", {
+ skip_if_not_installed("zinbwave")
expect_output(show(params), "A Params object of class ZINBParams")
})
test_that("nGenes checks work", {
+ skip_if_not_installed("zinbwave")
expect_error(setParam(params, "nGenes", 1),
"nGenes cannot be set directly")
expect_error(setParam(params, "nCells", 1),
diff --git a/tests/testthat/test-mfa-simulate.R b/tests/testthat/test-mfa-simulate.R
index 877e0a9686460f9ec84fe107c0fb1397da969723..4ae5c7b43cfd7808c8f18ad0c3da518e40c874e8 100644
--- a/tests/testthat/test-mfa-simulate.R
+++ b/tests/testthat/test-mfa-simulate.R
@@ -1,6 +1,7 @@
context("mfa simulation")
test_that("mfa simulation output is valid", {
+ skip_if_not_installed("mfa")
expect_true(validObject(mfaSimulate()))
expect_true(validObject(mfaSimulate(dropout.present = TRUE)))
})
diff --git a/tests/testthat/test-pheno-simulate.R b/tests/testthat/test-pheno-simulate.R
index f67a25e72e0ca8cd8ef82537f83a752ae23a429a..13e6aab87703df14a0244876ce8fc0e14dfb178c 100644
--- a/tests/testthat/test-pheno-simulate.R
+++ b/tests/testthat/test-pheno-simulate.R
@@ -1,5 +1,6 @@
context("PhenoPath simulation")
test_that("PhenoPath simulation output is valid", {
+ skip_if_not_installed("phenopath")
expect_true(validObject(phenoSimulate()))
})
diff --git a/tests/testthat/test-phenoEstimate.R b/tests/testthat/test-phenoEstimate.R
index 402d78164c1ad0e9491097aaa3cc978ab015e44d..d0ffc66d0aa485d6d2ebb38c99cca59f54dded1f 100644
--- a/tests/testthat/test-phenoEstimate.R
+++ b/tests/testthat/test-phenoEstimate.R
@@ -4,6 +4,7 @@ library(scater)
data("sc_example_counts")
test_that("phenoEstimate works", {
+ skip_if_not_installed("phenopath")
params <- phenoEstimate(sc_example_counts)
expect_true(validObject(params))
})
diff --git a/tests/testthat/test-scDD-simulate.R b/tests/testthat/test-scDD-simulate.R
index 1c727e2f50d98d21cf3c6287b4dd05d336ee86c4..8580640cad86f7c0b43bf7c329a83bd4442949e4 100644
--- a/tests/testthat/test-scDD-simulate.R
+++ b/tests/testthat/test-scDD-simulate.R
@@ -1,7 +1,8 @@
context("scDD simulation")
test_that("scDD simulation output is valid", {
+ skip_if_not_installed("scDD")
params <- newSCDDParams(nDE = 5, nDP = 5, nDM = 5, nDB = 5, nEE = 5,
nEP = 5)
expect_true(validObject(scDDSimulate(params)))
-})
\ No newline at end of file
+})
diff --git a/tests/testthat/test-sparseDC-simulate.R b/tests/testthat/test-sparseDC-simulate.R
index 7edef92b9c691a480eecd58721994098e2fb259a..35653447fd07e6e233fbbcbe0b62242f8b0670a6 100644
--- a/tests/testthat/test-sparseDC-simulate.R
+++ b/tests/testthat/test-sparseDC-simulate.R
@@ -1,5 +1,6 @@
context("SparseDC simulation")
test_that("SparseDC simulation output is valid", {
+ skip_if_not_installed("SparseDC")
expect_true(validObject(sparseDCSimulate()))
})
diff --git a/tests/testthat/test-sparseDCEstimate.R b/tests/testthat/test-sparseDCEstimate.R
index 3bdc50b7962a008a1a8db7630144d7560192d7ac..2e18499c025c42db212159e4e92787ea730aa189 100644
--- a/tests/testthat/test-sparseDCEstimate.R
+++ b/tests/testthat/test-sparseDCEstimate.R
@@ -4,6 +4,7 @@ library(scater)
data("sc_example_counts")
test_that("sparseDCEstimate works", {
+ skip_if_not_installed("SparseDC")
set.seed(1)
conditions <- sample(1:2, ncol(sc_example_counts), replace = TRUE)
params <- sparseDCEstimate(sc_example_counts, conditions,
diff --git a/tests/testthat/test-zinb-simulate.R b/tests/testthat/test-zinb-simulate.R
index 80b2b1c5bcd8062be039f7a2260458920353d6de..9d7d3cf17204de62002ad124d2a2fdfdb6fab577 100644
--- a/tests/testthat/test-zinb-simulate.R
+++ b/tests/testthat/test-zinb-simulate.R
@@ -1,5 +1,6 @@
context("ZINB-WaVE simulation")
test_that("ZINB-WaVE simulation output is valid", {
+ skip_if_not_installed("zinbwave")
expect_true(validObject(zinbSimulate()))
})
diff --git a/vignettes/splatter.Rmd b/vignettes/splatter.Rmd
index 46135d2e4fdf454725c873ce43e48695db308187..af3eeff28682164c346d4be2b23230396de48a23 100644
--- a/vignettes/splatter.Rmd
+++ b/vignettes/splatter.Rmd
@@ -29,14 +29,15 @@ introduction to Splatter's functionality.
Splatter can be installed from Bioconductor:
```{r install, eval = FALSE}
-source("https://bioconductor.org/biocLite.R")
-biocLite("splatter")
+if (!requireNamespace("BiocManager", quietly=TRUE))
+ install.packages("BiocManager")
+BiocManager::install("splatter")
```
To install the most recent development version from Github use:
```{r install-github, eval = FALSE}
-biocLite("Oshlack/splatter", dependencies = TRUE,
+BiocManager::install("Oshlack/splatter", dependencies = TRUE,
build_vignettes = TRUE)
```
@@ -282,7 +283,7 @@ in `scater`. For example we can make a PCA plot:
```{r pca}
# Use scater to calculate logcounts
-sim <- normalise(sim)
+sim <- normalize(sim)
# Plot PCA
plotPCA(sim)
```
@@ -342,7 +343,7 @@ printing progress messages.)
```{r groups}
sim.groups <- splatSimulate(group.prob = c(0.5, 0.5), method = "groups",
verbose = FALSE)
-sim.groups <- normalise(sim.groups)
+sim.groups <- normalize(sim.groups)
plotPCA(sim.groups, colour_by = "Group")
```
@@ -361,7 +362,7 @@ method.
```{r paths}
sim.paths <- splatSimulate(method = "paths", verbose = FALSE)
-sim.paths <- normalise(sim.paths)
+sim.paths <- normalize(sim.paths)
plotPCA(sim.paths, colour_by = "Step")
```
@@ -381,7 +382,7 @@ cells are in each batch:
```{r batches}
sim.batches <- splatSimulate(batchCells = c(50, 50), verbose = FALSE)
-sim.batches <- normalise(sim.batches)
+sim.batches <- normalize(sim.batches)
plotPCA(sim.batches, colour_by = "Batch")
```
@@ -395,7 +396,7 @@ that we aren't interested in (batch) and the wanted variation we are looking for
```{r batch-groups}
sim.groups <- splatSimulate(batchCells = c(50, 50), group.prob = c(0.5, 0.5),
method = "groups", verbose = FALSE)
-sim.groups <- normalise(sim.groups)
+sim.groups <- normalize(sim.groups)
plotPCA(sim.groups, shape_by = "Batch", colour_by = "Group")
```
@@ -503,7 +504,7 @@ number of expressed genes against the library size:
```{r comparison-libsize-features}
library("ggplot2")
ggplot(comparison$PhenoData,
- aes(x = total_counts, y = total_features, colour = Dataset)) +
+ aes(x = total_counts, y = total_features_by_counts, colour = Dataset)) +
geom_point()
```