diff --git a/DESCRIPTION b/DESCRIPTION
index af80af7822f107b89bc93841b30e293bfd0fd438..8d6ed5f3936c6bef47b00f601fae2b6db5231f65 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: splatter
Type: Package
Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 1.1.6
-Date: 2017-10-02
+Version: 1.1.7
+Date: 2017-10-05
Author: Luke Zappia
Authors@R:
c(person("Luke", "Zappia", role = c("aut", "cre"),
diff --git a/NEWS.md b/NEWS.md
index cef16188426f0dbc0e04c451e242d5358ef872d7..9066d35406e9f8ecbae08b624d504c27a55f56d7 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,9 @@
+## Version 1.1.7 (2017-10-05)
+
+* Add PhenoPath simulation
+* Add ZINB-WaVE simulation
+* Adjust mfaSimulate output
+
## Version 1.1.6 (2017-10-02)
* Update scDD version
diff --git a/R/mfa-simulate.R b/R/mfa-simulate.R
index bca30e7900f9b8c41cb5d65c531fa296df7704d3..b208bdeacd10aea2972644ad9aa27321618084ff 100644
--- a/R/mfa-simulate.R
+++ b/R/mfa-simulate.R
@@ -59,11 +59,12 @@ mfaSimulate <- function(params = newMFAParams(), verbose = TRUE, ...) {
gene.names <- paste0("Gene", seq_len(nGenes))
exprs <- t(mfa.sim$X)
+ rownames(exprs) <- gene.names
+ colnames(exprs) <- cell.names
+
counts <- 2 ^ exprs - 1
counts[counts < 0] <- 0
counts <- round(counts)
- rownames(counts) <- gene.names
- colnames(counts) <- cell.names
cells <- data.frame(Cell = cell.names,
Branch = mfa.sim$branch,
diff --git a/R/zinb-estimate.R b/R/zinb-estimate.R
index 217283c8e91058b5199ee67462b5437b0ecbce0b..2a14443ccba5949f9cfba69730a0887b7b4ecdb3 100644
--- a/R/zinb-estimate.R
+++ b/R/zinb-estimate.R
@@ -28,9 +28,11 @@
#' @return ZINBParams object containing the estimated parameters.
#'
#' @examples
+#' \dontrun{
#' data("sc_example_counts")
#' params <- zinbEstimate(sc_example_counts)
#' params
+#' }
#' @importFrom BiocParallel SerialParam
#' @export
zinbEstimate <- function(counts, design.samples = NULL, design.genes = NULL,
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 66805598959cbcf95237f1db8c4cd79fd4c19143..74aacfba6c37242e8a30deae1f51dd0cf058329a 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -15,7 +15,7 @@ reference:
- '`MFAParams`'
- '`newParams`'
- '`Params`'
- - '`phenoParams`'
+ - '`PhenoParams`'
- '`SCDDParams`'
- '`SimpleParams`'
- '`SplatParams`'
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 35e1b8d093308f4710b79893b79f3cd3c30aa4c5..3a8201b24fa0eb72c1e919ca03dd7abcd1891335 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -96,7 +96,7 @@
</header>
<div class="page-header">
- <h1>Articles <small>version 1.1.6</small></h1>
+ <h1>Articles <small>version 1.1.7</small></h1>
</div>
<div class="row">
diff --git a/docs/articles/splatter.html b/docs/articles/splatter.html
index fa8212094a6c15b5dbaa1e53cd87c3d1eacaf790..93aae153288311a4c6e9d4504519e98587ba1ae0 100644
--- a/docs/articles/splatter.html
+++ b/docs/articles/splatter.html
@@ -76,7 +76,7 @@
<h1>Introduction to Splatter</h1>
<h4 class="author">Luke Zappia</h4>
- <h4 class="date">2017-10-02</h4>
+ <h4 class="date">2017-10-05</h4>
</div>
@@ -317,7 +317,7 @@ params</code></pre></div>
##
## Global:
## (Genes) (Cells) [Seed]
-## 10000 100 395011
+## 10000 100 882480
##
## 27 additional parameters
##
@@ -390,7 +390,7 @@ params</code></pre></div>
##
## Global:
## (GENES) (Cells) [Seed]
-## 8000 100 395011
+## 8000 100 882480
##
## 27 additional parameters
##
@@ -501,45 +501,45 @@ sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class=
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Access the counts</span>
<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>]</code></pre></div>
<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
-## Gene1 0 402 19 311 0
-## Gene2 0 12 25 252 0
-## Gene3 0 0 0 3 0
-## Gene4 0 0 0 14 3
-## Gene5 0 95 0 7 0</code></pre>
+## Gene1 0 0 2 0 22
+## Gene2 25024 156 1 24 0
+## Gene3 185 126 2 0 0
+## Gene4 17 0 1 0 0
+## Gene5 0 0 0 0 0</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Information about genes</span>
<span class="kw">head</span>(<span class="kw">rowData</span>(sim))</code></pre></div>
<pre><code>## DataFrame with 6 rows and 4 columns
-## Gene BaseGeneMean OutlierFactor GeneMean
-## <factor> <numeric> <numeric> <numeric>
-## 1 Gene1 210.1089973 1 210.1089973
-## 2 Gene2 45.3776510 1 45.3776510
-## 3 Gene3 0.6516767 1 0.6516767
-## 4 Gene4 74.2508364 1 74.2508364
-## 5 Gene5 13.9862181 1 13.9862181
-## 6 Gene6 6.9628144 1 6.9628144</code></pre>
+## Gene BaseGeneMean OutlierFactor GeneMean
+## <factor> <numeric> <numeric> <numeric>
+## 1 Gene1 5.975143e+00 1 5.975143e+00
+## 2 Gene2 6.047020e+02 1 6.047020e+02
+## 3 Gene3 3.407454e+02 1 3.407454e+02
+## 4 Gene4 1.041869e+00 1 1.041869e+00
+## 5 Gene5 6.429022e-03 1 6.429022e-03
+## 6 Gene6 5.051255e+02 1 5.051255e+02</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Information about cells</span>
<span class="kw">head</span>(<span class="kw">colData</span>(sim))</code></pre></div>
<pre><code>## DataFrame with 6 rows and 3 columns
## Cell Batch ExpLibSize
## <factor> <character> <numeric>
-## Cell1 Cell1 Batch1 1187108.5
-## Cell2 Cell2 Batch1 600191.4
-## Cell3 Cell3 Batch1 688730.7
-## Cell4 Cell4 Batch1 256123.3
-## Cell5 Cell5 Batch1 278401.4
-## Cell6 Cell6 Batch1 385774.4</code></pre>
+## Cell1 Cell1 Batch1 413957.7
+## Cell2 Cell2 Batch1 476887.9
+## Cell3 Cell3 Batch1 367310.0
+## Cell4 Cell4 Batch1 147775.6
+## Cell5 Cell5 Batch1 193681.3
+## Cell6 Cell6 Batch1 590802.3</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Gene by cell matrices</span>
<span class="kw">names</span>(<span class="kw">assays</span>(sim))</code></pre></div>
<pre><code>## [1] "BatchCellMeans" "BaseCellMeans" "BCV" "CellMeans"
## [5] "TrueCounts" "counts"</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Example of cell means matrix</span>
<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>]</code></pre></div>
-<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
-## Gene1 8.281664e-05 4.086520e+02 1.480335e+01 306.253250 1.453613e-02
-## Gene2 2.394664e-13 1.278677e+01 2.171332e+01 278.515526 3.609326e-11
-## Gene3 7.817149e-21 5.174676e-13 3.583580e-01 2.217521 9.095013e-52
-## Gene4 1.737589e-08 4.257554e-11 1.005446e-07 16.146507 3.822216e+00
-## Gene5 2.822351e-22 1.094278e+02 9.679284e-05 8.000741 1.988529e-05</code></pre>
+<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
+## Gene1 4.400164e-01 6.304542e-02 1.10406696 8.139464e-10 2.335664e+01
+## Gene2 2.526252e+04 1.595860e+02 0.03470768 2.065810e+01 6.231519e-02
+## Gene3 1.899993e+02 1.229909e+02 1.03528470 4.606624e-03 1.921180e-06
+## Gene4 1.421395e+01 5.383794e-10 0.34678991 7.669389e-03 2.339044e-18
+## Gene5 3.522450e-87 2.621383e-03 0.01039596 3.410733e-82 1.870620e-46</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"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">plotPCA</span>(sim, <span class="dt">exprs_values =</span> <span class="st">"counts"</span>)</code></pre></div>
<p><img src="splatter_files/figure-html/pca-1.png" width="576" style="display: block; margin: auto;"></p>
@@ -640,39 +640,43 @@ sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class=
<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"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="../reference/listSims.html">listSims</a></span>()</code></pre></div>
-<pre><code>## Splatter currently contains 8 simulations
+<pre><code>## Splatter currently contains 9 simulations
##
## Splat (splat)
-## DOI: Github:
-## The Splat simulation generates means from a gamma distribution, adjusts them for BCV and generates counts from a gamma-poisson. Dropout can be optionally added.
+## DOI: GitHub:
+## The Splat simulation generates means from a gamma distribution, adjusts them for BCV and generates counts from a gamma-poisson. Dropout and batch effects can be optionally added.
##
## Splat Single (splatSingle)
-## DOI: Github:
+## DOI: GitHub:
## The Splat simulation with a single population.
##
## Splat Groups (splatGroups)
-## DOI: Github:
+## DOI: GitHub:
## The Splat simulation with multiple groups. Each group can have it's own differential expression probability and fold change distribution.
##
## Splat Paths (splatPaths)
-## DOI: Github:
+## DOI: GitHub:
## The Splat simulation with differentiation paths. Each path can have it's own length, skew and probability. Genes can change in non-linear ways.
##
## Simple (simple)
-## DOI: Github:
+## DOI: GitHub:
## A simple simulation with gamma means and negative binomial counts.
##
## Lun (lun)
-## DOI: 10.1186/s13059-016-0947-7 Github: MarioniLab/Deconvolution2016
+## DOI: 10.1186/s13059-016-0947-7 GitHub: MarioniLab/Deconvolution2016
## Gamma distributed means and negative binomial counts. Cells are given a size factor and differential expression can be simulated with fixed fold changes.
##
## Lun 2 (lun2)
-## DOI: 10.1101/073973 Github: MarioniLab/PlateEffects2016
+## DOI: 10.1101/073973 GitHub: MarioniLab/PlateEffects2016
## Negative binomial counts where the means and dispersions have been sampled from a real dataset. The core feature of the Lun 2 simulation is the addition of plate effects. Differential expression can be added between two groups of plates and optionally a zero-inflated negative-binomial can be used.
##
## scDD (scDD)
-## DOI: 10.1186/s13059-016-1077-y Github: kdkorthauer/scDD
-## The scDD simulation samples a given dataset and can simulate differentially expressed and differentially distributed genes between two conditions.</code></pre>
+## DOI: 10.1186/s13059-016-1077-y GitHub: kdkorthauer/scDD
+## The scDD simulation samples a given dataset and can simulate differentially expressed and differentially distributed genes between two conditions.
+##
+## mfa (mfa)
+## DOI: 10.12688/wellcomeopenres.11087.1 GitHub: kieranrcampbell/mfa
+## The mfa simulation produces a bifurcating pseudotime trajectory. This can optionally include genes with transient changes in expression and added dropout.</code></pre>
<p>(or more conveniently for the vignette as a table)</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">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>))</code></pre></div>
<table class="table">
@@ -680,7 +684,7 @@ sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class=
<th align="left">Name</th>
<th align="left">Prefix</th>
<th align="left">DOI</th>
-<th align="left">Github</th>
+<th align="left">GitHub</th>
<th align="left">Description</th>
</tr></thead>
<tbody>
@@ -689,7 +693,7 @@ sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class=
<td align="left">splat</td>
<td align="left"></td>
<td align="left"></td>
-<td align="left">The Splat simulation generates means from a gamma distribution, adjusts them for BCV and generates counts from a gamma-poisson. Dropout can be optionally added.</td>
+<td align="left">The Splat simulation generates means from a gamma distribution, adjusts them for BCV and generates counts from a gamma-poisson. Dropout and batch effects can be optionally added.</td>
</tr>
<tr class="even">
<td align="left">Splat Single</td>
@@ -740,6 +744,13 @@ sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class=
<td align="left">kdkorthauer/scDD</td>
<td align="left">The scDD simulation samples a given dataset and can simulate differentially expressed and differentially distributed genes between two conditions.</td>
</tr>
+<tr class="odd">
+<td align="left">mfa</td>
+<td align="left">mfa</td>
+<td align="left">10.12688/wellcomeopenres.11087.1</td>
+<td align="left">kieranrcampbell/mfa</td>
+<td align="left">The mfa simulation produces a bifurcating pseudotime trajectory. This can optionally include genes with transient changes in expression and added dropout.</td>
+</tr>
</tbody>
</table>
<p>Each simulation has it’s own prefix which gives the name of the functions associated with that simulation. For example the prefix for the simple simulation is <code>simple</code> so it would store it’s parameters in a <code>SimpleParams</code> object that can be created using <code><a href="../reference/newParams.html">newSimpleParams()</a></code> or estimated from real data using <code><a href="../reference/simpleEstimate.html">simpleEstimate()</a></code>. To simulate data using that simulation you would use <code><a href="../reference/simpleSimulate.html">simpleSimulate()</a></code>. Each simulation returns a <code>SingleCellExperiment</code> object with intermediate values similar to that returned by <code><a href="../reference/splatSimulate.html">splatSimulate()</a></code>. For more detailed information on each simulation see the appropriate help page (eg. <code><a href="../reference/simpleSimulate.html">?simpleSimulate</a></code> for information on how the simple simulation works or <code><a href="../reference/lun2Estimate.html">? lun2Estimate</a></code> for details of how the Lun 2 simulation estimates parameters) or refer to the appropriate paper or package.</p>
@@ -752,23 +763,23 @@ sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class=
sim <-<span class="st"> </span><span class="kw"><a href="../reference/addGeneLengths.html">addGeneLengths</a></span>(sim)
<span class="kw">head</span>(<span class="kw">rowData</span>(sim))</code></pre></div>
<pre><code>## DataFrame with 6 rows and 3 columns
-## Gene GeneMean Length
-## <factor> <numeric> <numeric>
-## 1 Gene1 10.53439855 5193
-## 2 Gene2 2.10971396 4499
-## 3 Gene3 4.47004567 5511
-## 4 Gene4 0.19267026 3381
-## 5 Gene5 0.06672189 2570
-## 6 Gene6 0.87920676 806</code></pre>
+## Gene GeneMean Length
+## <factor> <numeric> <numeric>
+## 1 Gene1 1.60506942 1775
+## 2 Gene2 2.17500094 4361
+## 3 Gene3 1.16851643 2915
+## 4 Gene4 0.01040965 16794
+## 5 Gene5 0.06781127 948
+## 6 Gene6 3.03114500 3089</code></pre>
<p>We can then use <code>scater</code> to calculate TPM:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">tpm</span>(sim) <-<span class="st"> </span><span class="kw">calculateTPM</span>(sim, <span class="kw">rowData</span>(sim)<span class="op">$</span>Length)
<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>]</code></pre></div>
<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
-## Gene1 0.22854912 0.16875798 0.23480191 0.20342087 0.21439203
-## Gene2 0.04946331 0.01623250 0.03387770 0.03354284 0.03299512
-## Gene3 0.05384030 0.07951009 0.02765665 0.04107491 0.02693613
+## Gene1 0.08215535 0.04069785 0.08360619 0.08404271 0.08403017
+## Gene2 0.03343860 0.01656470 0.13611647 0.00000000 0.06840337
+## Gene3 0.00000000 0.02478171 0.05090943 0.02558762 0.02558380
## Gene4 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
-## Gene5 0.00000000 0.00000000 0.00000000 0.02935977 0.00000000</code></pre>
+## Gene5 0.00000000 0.07620114 0.00000000 0.00000000 0.00000000</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">
@@ -861,7 +872,7 @@ cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumenta
## [8] methods base
##
## other attached packages:
-## [1] splatter_1.1.5 scater_1.5.16
+## [1] splatter_1.1.6 scater_1.5.16
## [3] SingleCellExperiment_0.99.4 SummarizedExperiment_1.7.10
## [5] DelayedArray_0.3.21 matrixStats_0.52.2
## [7] GenomicRanges_1.29.14 GenomeInfoDb_1.13.4
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diff --git a/docs/news/index.html b/docs/news/index.html
index 8c92674a484b15ac19a70e12947eee4d8eb62938..a33131ead1bdf1d58d7987e3f3ff5774a253791d 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -103,6 +103,15 @@
</div>
<div class="contents">
+ <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 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>
@@ -439,6 +448,7 @@
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
+ <li><a href="#version-1-1-7-2017-10-05">1.1.7</a></li>
<li><a href="#version-1-1-6-2017-10-02">1.1.6</a></li>
<li><a href="#version-1-1-5-2017-09-13">1.1.5</a></li>
<li><a href="#version-1-1-4-2017-08-04">1.1.4</a></li>
diff --git a/docs/reference/PhenoParams.html b/docs/reference/PhenoParams.html
new file mode 100644
index 0000000000000000000000000000000000000000..79dce00cb9cb926c15759b34cfa0740bcdefcd10
--- /dev/null
+++ b/docs/reference/PhenoParams.html
@@ -0,0 +1,154 @@
+<!-- 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">
+
+<title>The PhenoParams class — PhenoParams • Splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
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+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
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+<![endif]-->
+
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+ })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
+
+ ga('create', 'UA-52309538-4', 'auto');
+ ga('send', 'pageview');
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+ <header>
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+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <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>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
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+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
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+ </div><!--/.nav-collapse -->
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+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>The PhenoParams class</h1>
+ </div>
+
+
+ <p>S4 class that holds parameters for the PhenoPath simulation.</p>
+
+
+
+ <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'>
+ <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>
+ <dt><code>[n.de]</code></dt><dd><p>Number of genes to simulate from the differential
+ expression regime</p></dd>
+ <dt><code>[n.pst]</code></dt><dd><p>Number of genes to simulate from the pseudotime
+ regime</p></dd>
+ <dt><code>[n.pst.beta]</code></dt><dd><p>Number of genes to simulate from the
+ pseudotime + beta interactions regime</p></dd>
+ <dt><code>[n.de.pst.beta]</code></dt><dd><p>Number of genes to simulate from the
+ differential expression + pseudotime + interactions regime</p></dd>
+</dl>
+ <p>The parameters not shown in brackets can be estimated from real data using
+<code><a href='phenoEstimate.html'>phenoEstimate</a></code>. For details of the PhenoPath simulation
+see <code><a href='phenoSimulate.html'>phenoSimulate</a></code>.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+
+ <li><a href="#parameters">Parameters</a></li>
+ </ul>
+
+ </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://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/ZINBParams.html b/docs/reference/ZINBParams.html
new file mode 100644
index 0000000000000000000000000000000000000000..531f0b99428c90fb54fea5a6c93b55cc50b3cf8b
--- /dev/null
+++ b/docs/reference/ZINBParams.html
@@ -0,0 +1,151 @@
+<!-- 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">
+
+<title>The ZINBParams class — ZINBParams • 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">
+
+<!-- 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(){
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+ 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');
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+ <div class="container template-reference-topic">
+ <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>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </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>
+<li>
+ <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>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>The ZINBParams class</h1>
+ </div>
+
+
+ <p>S4 class that holds parameters for the ZINB-WaVE simulation.</p>
+
+
+
+ <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'>
+ <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>
+ <dt><code>model</code></dt><dd><p>Object describing a ZINB model.</p></dd>
+</dl>
+ <p>The majority of the parameters for this simulation are stored in a
+<code><a href='http://www.rdocumentation.org/packages/zinbwave/topics/ZinbModel-class'>ZinbModel</a></code> object. Please refer to the documentation
+for this class and its constructor(<code><a href='http://www.rdocumentation.org/packages/zinbwave/topics/zinbModel'>zinbModel</a></code>) for
+details about all the parameters.</p>
+<p>The parameters not shown in brackets can be estimated from real data using
+<code><a href='zinbEstimate.html'>zinbEstimate</a></code>. For details of the ZINB-WaVE simulation
+see <code><a href='zinbSimulate.html'>zinbSimulate</a></code>.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+
+ <li><a href="#parameters">Parameters</a></li>
+ </ul>
+
+ </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://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/addGeneLengths.html b/docs/reference/addGeneLengths.html
index 7e1c743953665b18c481918dedb2e09ca5a0aafb..9fa10ffe6a1724705b175161d6e785c1e0715034 100644
--- a/docs/reference/addGeneLengths.html
+++ b/docs/reference/addGeneLengths.html
@@ -154,14 +154,14 @@ 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 0.02190272 2415
-#> 2 Gene2 0.42347583 4759
-#> 3 Gene3 0.09714480 5381
-#> 4 Gene4 0.77350851 4799
-#> 5 Gene5 1.78755781 4590
-#> 6 Gene6 0.06988693 925</div><div class='input'># Sample method (human coding genes)
+#> Gene GeneMean Length
+#> <factor> <numeric> <numeric>
+#> 1 Gene1 0.8455684 1284
+#> 2 Gene2 0.1606091 5127
+#> 3 Gene3 6.7083234 1847
+#> 4 Gene4 0.2917321 2194
+#> 5 Gene5 1.4748643 1567
+#> 6 Gene6 0.0326816 7629</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>)
diff --git a/docs/reference/index.html b/docs/reference/index.html
index aeeac57b4384d872ff84283a807598ade777c55e..3697b90316d31166e41d778508a961047ef7f515 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -100,7 +100,7 @@
<div class="page-header">
<h1>
Reference
- <small>version 1.1.6</small>
+ <small>version 1.1.7</small>
</h1>
</div>
@@ -152,7 +152,7 @@
</tr><tr>
<!-- -->
<td>
- <p><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">newSCDDParams</a></code> <code><a href="newParams.html">newSimpleParams</a></code> <code><a href="newParams.html">newSplatParams</a></code> </p>
+ <p><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">newSplatParams</a></code> <code><a href="newParams.html">newZINBParams</a></code> </p>
</td>
<td><p>New Params</p></td>
</tr><tr>
@@ -161,6 +161,12 @@
<p></p>
</td>
<td><p>The Params virtual class</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p></p>
+ </td>
+ <td><p>The PhenoParams class</p></td>
</tr><tr>
<!-- -->
<td>
@@ -191,6 +197,12 @@
<p><code><a href="setParams.html">setParams</a></code> </p>
</td>
<td><p>Set parameters</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p></p>
+ </td>
+ <td><p>The ZINBParams class</p></td>
</tr>
</tbody><tbody>
<tr>
@@ -217,6 +229,12 @@
<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>
@@ -265,6 +283,12 @@
<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="zinbEstimate.html">zinbEstimate</a></code> </p>
+ </td>
+ <td><p>Estimate ZINB-WaVE simulation parameters</p></td>
</tr>
</tbody><tbody>
<tr>
@@ -291,6 +315,12 @@
<p><code><a href="mfaSimulate.html">mfaSimulate</a></code> </p>
</td>
<td><p>MFA simulation</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>
@@ -363,6 +393,12 @@
<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="zinbSimulate.html">zinbSimulate</a></code> </p>
+ </td>
+ <td><p>ZINB-WaVE simulation</p></td>
</tr>
</tbody><tbody>
<tr>
diff --git a/docs/reference/listSims.html b/docs/reference/listSims.html
index 5cbb9a4142bf6233f69ec2a324f2db153048b682..dca08b58960dfd1925bdb25b7db37f28e96a8060 100644
--- a/docs/reference/listSims.html
+++ b/docs/reference/listSims.html
@@ -124,7 +124,7 @@ displayed.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='fu'>listSims</span>()</div><div class='output co'>#> Splatter currently contains 9 simulations
+ <pre class="examples"><div class='input'><span class='fu'>listSims</span>()</div><div class='output co'>#> Splatter currently contains 11 simulations
#>
#> Splat (splat)
#> DOI: GitHub:
@@ -161,6 +161,14 @@ displayed.</p>
#> mfa (mfa)
#> DOI: 10.12688/wellcomeopenres.11087.1 GitHub: kieranrcampbell/mfa
#> The mfa simulation produces a bifurcating pseudotime trajectory. This can optionally include genes with transient changes in expression and added dropout.
+#>
+#> PhenoPath (pheno)
+#> DOI: 10.1101/159913 GitHub: kieranrcampbell/phenopath
+#> The PhenoPath simulation produces a pseudotime trajectory with different types of genes.
+#>
+#> ZINB-WaVE (zinb)
+#> DOI: 10.1101/125112 GitHub: drisso/zinbwave
+#> The ZINB-WaVE simulation simulates counts from a sophisticated zero-inflated negative-binomial distribution including cell and gene-level covariates.
#> </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
diff --git a/docs/reference/lunEstimate.html b/docs/reference/lunEstimate.html
index dacfa9b7c5500d613942dc015e7ca9423671fd57..4d3d97cd872674d7b8ac41b6fd430e77fa6eb8e0 100644
--- a/docs/reference/lunEstimate.html
+++ b/docs/reference/lunEstimate.html
@@ -146,7 +146,7 @@ for more details on the parameters.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 116529
+#> 2000 40 80751
#>
#> 9 additional parameters
#>
diff --git a/docs/reference/mfaEstimate.html b/docs/reference/mfaEstimate.html
index 92b8c0e31fff2175d299737aae38e27481b22000..86367e0bb4179d6ec5e7f6919ec418f9748ef277 100644
--- a/docs/reference/mfaEstimate.html
+++ b/docs/reference/mfaEstimate.html
@@ -147,7 +147,7 @@ details on the parameters.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 116529
+#> 2000 40 80751
#>
#> 4 additional parameters
#>
diff --git a/docs/reference/mfaSimulate.html b/docs/reference/mfaSimulate.html
index 317790982e28c307d4ad3876179e68d20a05777e..f0365d753ec6394242e02404a28ab09a3f01f52c 100644
--- a/docs/reference/mfaSimulate.html
+++ b/docs/reference/mfaSimulate.html
@@ -133,9 +133,10 @@
<p>This function is just a wrapper around <code><a href='http://www.rdocumentation.org/packages/mfa/topics/create_synthetic'>create_synthetic</a></code>
that takes a <code><a href='MFAParams.html'>MFAParams</a></code>, runs the simulation then converts the
-output to a <code><a href='http://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object.
-See <code><a href='http://www.rdocumentation.org/packages/mfa/topics/create_synthetic'>create_synthetic</a></code> and the mfa paper for more details
-about how the simulation works.</p>
+output from log-expression to counts and returns a
+<code><a href='http://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object. See
+<code><a href='http://www.rdocumentation.org/packages/mfa/topics/create_synthetic'>create_synthetic</a></code> and the mfa paper for more details about
+how the simulation works.</p>
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
diff --git a/docs/reference/newParams.html b/docs/reference/newParams.html
index 466518a4a390c0141791e48be6842c3bd0ef8e85..f4a4e70af542d39e7fd1ae5f96078a8115ba9684 100644
--- a/docs/reference/newParams.html
+++ b/docs/reference/newParams.html
@@ -112,11 +112,15 @@ Params subtypes.</p>
<span class='fu'>newMFAParams</span>(<span class='no'>...</span>)
+<span class='fu'>newPhenoParams</span>(<span class='no'>...</span>)
+
<span class='fu'>newSCDDParams</span>(<span class='no'>...</span>)
<span class='fu'>newSimpleParams</span>(<span class='no'>...</span>)
-<span class='fu'>newSplatParams</span>(<span class='no'>...</span>)</pre>
+<span class='fu'>newSplatParams</span>(<span class='no'>...</span>)
+
+<span class='fu'>newZINBParams</span>(<span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
<table class="ref-arguments">
diff --git a/docs/reference/phenoEstimate.html b/docs/reference/phenoEstimate.html
new file mode 100644
index 0000000000000000000000000000000000000000..60f7ec4bf34ab36f4a50ea70f7f269b1bb3a5b80
--- /dev/null
+++ b/docs/reference/phenoEstimate.html
@@ -0,0 +1,188 @@
+<!-- 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">
+
+<title>Estimate PhenoPath simulation parameters — phenoEstimate • 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">
+
+<!-- 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(){
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+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
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+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
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+
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+ </div><!--/.nav-collapse -->
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+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Estimate PhenoPath simulation parameters</h1>
+ </div>
+
+
+ <p>Estimate simulation parameters for the PhenoPath simulation from a real
+dataset.</p>
+
+
+ <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>())
+
+<span class='co'># S3 method for SingleCellExperiment</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>())
+
+<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>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>counts</th>
+ <td><p>either a counts matrix or an SingleCellExperiment object
+containing count data to estimate parameters from.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>PhenoParams object to store estimated values in.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>PhenoParams object containing the estimated parameters.</p>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>The <code>nGenes</code> and <code>nCells</code> parameters are taken from the size of the
+input data. The total number of genes is evenly divided into the four types.
+See <code><a href='PhenoParams.html'>PhenoParams</a></code> 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='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>phenoEstimate</span>(<span class='no'>sc_example_counts</span>)
+<span class='no'>params</span></div><div class='output co'>#> A Params object of class PhenoParams
+#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'.
+#>
+#> Global:
+#> (GENES) (CELLS) [Seed]
+#> 2000 40 80751
+#>
+#> 4 additional parameters
+#>
+#> Genes:
+#> [DE] [PST] [PST + BETA] [DE + PST + BETA]
+#> 500 500 500 500
+#> </div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#details">Details</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </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://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/phenoSimulate.html b/docs/reference/phenoSimulate.html
new file mode 100644
index 0000000000000000000000000000000000000000..1d84c2c4e049e029cefe5fc5ec6829f553cf4d12
--- /dev/null
+++ b/docs/reference/phenoSimulate.html
@@ -0,0 +1,186 @@
+<!-- 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">
+
+<title>PhenoPath simulation — phenoSimulate • 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">
+
+<!-- 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');
+
+</script>
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+ <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>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </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>
+<li>
+ <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>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>PhenoPath simulation</h1>
+ </div>
+
+
+ <p>Simulate counts from a pseudotime trajectory using the PhenoPath method.</p>
+
+
+ <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>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>params</th>
+ <td><p>PhenoParams object containing simulation parameters.</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>logical. Whether to print progress messages</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>any additional parameter settings to override what is provided in
+<code>params</code>.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SingleCellExperiment containing simulated counts</p>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>This function is just a wrapper around
+<code><a href='http://www.rdocumentation.org/packages/phenopath/topics/simulate_phenopath'>simulate_phenopath</a></code> that takes a
+<code><a href='PhenoParams.html'>PhenoParams</a></code>, runs the simulation then converts the
+output from log-expression to counts and returns a
+<code><a href='http://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object. The original
+simulated log-expression values are returned in the <code>LogExprs</code> asssay.
+See <code><a href='http://www.rdocumentation.org/packages/phenopath/topics/simulate_phenopath'>simulate_phenopath</a></code> and the PhenoPath paper for
+more details about how the simulation works.</p>
+
+ <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+ <p>Campbell K, Yau C. Uncovering genomic trajectories with heterogeneous genetic
+and environmental backgrounds across single-cells and populations. bioRxiv
+(2017).</p>
+<p>Paper: <a href='10.1101/159913'>10.1101/159913</a></p>
+<p>Code: <a href='https://github.com/kieranrcampbell/phenopath'>https://github.com/kieranrcampbell/phenopath</a></p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>phenoSimulate</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'>
+</div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#details">Details</a></li>
+
+ <li><a href="#references">References</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </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://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/setParam.html b/docs/reference/setParam.html
index 92e0d87fd12b02dce1085e34d77af3c21c35c64d..99335c81d2b59cea9716a897ff877b6b8bf887f7 100644
--- a/docs/reference/setParam.html
+++ b/docs/reference/setParam.html
@@ -116,10 +116,16 @@
<span class='co'># S4 method for Params</span>
<span class='fu'>setParam</span>(<span class='no'>object</span>, <span class='no'>name</span>, <span class='no'>value</span>)
+<span class='co'># S4 method for PhenoParams</span>
+<span class='fu'>setParam</span>(<span class='no'>object</span>, <span class='no'>name</span>, <span class='no'>value</span>)
+
<span class='co'># S4 method for SCDDParams</span>
<span class='fu'>setParam</span>(<span class='no'>object</span>, <span class='no'>name</span>, <span class='no'>value</span>)
<span class='co'># S4 method for SplatParams</span>
+<span class='fu'>setParam</span>(<span class='no'>object</span>, <span class='no'>name</span>, <span class='no'>value</span>)
+
+<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>
@@ -151,7 +157,7 @@
#>
#> Global:
#> (GENES) (Cells) [Seed]
-#> 100 100 116529
+#> 100 100 80751
#>
#> 3 additional parameters
#>
diff --git a/docs/reference/setParams.html b/docs/reference/setParams.html
index 572eb144908524870a3f6732525831787b8ddcbb..fce88df4cb077ae9e146819f48ea87d99bfb503b 100644
--- a/docs/reference/setParams.html
+++ b/docs/reference/setParams.html
@@ -146,7 +146,7 @@ them manually), see examples.</p>
#>
#> Global:
#> (Genes) (Cells) [Seed]
-#> 10000 100 116529
+#> 10000 100 80751
#>
#> 3 additional parameters
#>
@@ -164,7 +164,7 @@ them manually), see examples.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 1000 50 116529
+#> 1000 50 80751
#>
#> 3 additional parameters
#>
@@ -182,7 +182,7 @@ them manually), see examples.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 1000 50 116529
+#> 1000 50 80751
#>
#> 3 additional parameters
#>
diff --git a/docs/reference/simpleEstimate.html b/docs/reference/simpleEstimate.html
index 0b41b8ca6ac6acfbc01d7f7e4cd00ed3bb1c5df7..4b84b6729feb6a544eb9cf305f59a0e9c76ad8ab 100644
--- a/docs/reference/simpleEstimate.html
+++ b/docs/reference/simpleEstimate.html
@@ -149,7 +149,7 @@ details on the parameters.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 116529
+#> 2000 40 80751
#>
#> 3 additional parameters
#>
diff --git a/docs/reference/splatEstimate.html b/docs/reference/splatEstimate.html
index 8c1698417321424ba4e47c26df98b5c377f26c30..93bca84e612a8ad0975e6d8600f9d0b841b9e4de 100644
--- a/docs/reference/splatEstimate.html
+++ b/docs/reference/splatEstimate.html
@@ -149,7 +149,7 @@ containing count data to estimate parameters from.</p></td>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 116529
+#> 2000 40 80751
#>
#> 27 additional parameters
#>
diff --git a/docs/reference/summariseDiff.html b/docs/reference/summariseDiff.html
index 3367151b4f4f74cdbead6edee6a4ed17f0de9b06..236c83c1bc918da684a9a17b3ae045ada6e97e6d 100644
--- a/docs/reference/summariseDiff.html
+++ b/docs/reference/summariseDiff.html
@@ -127,19 +127,19 @@ Error (RMSE) for the various properties and ranks them.</p>
<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>)
<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 2.288457 NaN 1 2.361992 NaN
-#> 2 Splat Variance 9.864920 NaN 1 9.885907 NaN
-#> 3 Splat ZerosGene 30.000000 NaN 1 38.245000 NaN
-#> 4 Splat MeanVar 9.311683 NaN 1 11.773079 NaN
-#> 5 Splat MeanZeros 40.000000 NaN 1 41.455000 NaN
-#> 6 Splat LibSize 59924.000000 NaN 1 60889.500000 NaN
+#> 1 Splat Mean 2.338299 NaN 1 2.392073 NaN
+#> 2 Splat Variance 11.506849 NaN 1 10.222706 NaN
+#> 3 Splat ZerosGene 30.000000 NaN 1 38.780000 NaN
+#> 4 Splat MeanVar 9.588721 NaN 1 11.820910 NaN
+#> 5 Splat MeanZeros 45.000000 NaN 1 42.060000 NaN
+#> 6 Splat LibSize 55543.500000 NaN 1 58282.850000 NaN
#> MAERank RMSE RMSEScaled RMSERank
-#> 1 1 2.911241 NaN 1
-#> 2 1 12.576504 NaN 1
-#> 3 1 43.466366 NaN 1
-#> 4 1 14.872900 NaN 1
-#> 5 1 51.016909 NaN 1
-#> 6 1 62360.840953 NaN 1</div></pre>
+#> 1 1 2.907697 NaN 1
+#> 2 1 12.865170 NaN 1
+#> 3 1 44.006818 NaN 1
+#> 4 1 14.953873 NaN 1
+#> 5 1 51.575673 NaN 1
+#> 6 1 59902.661935 NaN 1</div></pre>
</div>
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<h2>Contents</h2>
diff --git a/docs/reference/zinbEstimate.html b/docs/reference/zinbEstimate.html
new file mode 100644
index 0000000000000000000000000000000000000000..29da734f978e6a770a8f471dfec8dcffd0546992
--- /dev/null
+++ b/docs/reference/zinbEstimate.html
@@ -0,0 +1,285 @@
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+ <div class="page-header">
+ <h1>Estimate ZINB-WaVE simulation parameters</h1>
+ </div>
+
+
+ <p>Estimate simulation parameters for the ZINB-WaVE simulation from a real
+dataset.</p>
+
+
+ <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'>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>
+
+ <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>
+ <th>counts</th>
+ <td><p>either a counts matrix or a SingleCellExperiment object
+containing count data to estimate parameters from.</p></td>
+ </tr>
+ <tr>
+ <th>design.samples</th>
+ <td><p>design matrix of sample-level covariates.</p></td>
+ </tr>
+ <tr>
+ <th>design.genes</th>
+ <td><p>design matrix of gene-level covariates.</p></td>
+ </tr>
+ <tr>
+ <th>common.disp</th>
+ <td><p>logical. Whether or not a single dispersion for all
+features is estimated.</p></td>
+ </tr>
+ <tr>
+ <th>iter.init</th>
+ <td><p>number of iterations to use for initalization.</p></td>
+ </tr>
+ <tr>
+ <th>iter.opt</th>
+ <td><p>number of iterations to use for optimization.</p></td>
+ </tr>
+ <tr>
+ <th>stop.opt</th>
+ <td><p>stopping criterion for optimization.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>ZINBParams object to store estimated values in.</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>logical. Whether to print progress messages.</p></td>
+ </tr>
+ <tr>
+ <th>BPPARAM</th>
+ <td><p>A <code><a href='http://www.rdocumentation.org/packages/BiocParallel/topics/BiocParallelParam-class'>BiocParallelParam</a></code> instance
+giving the parallel back-end to be used. Default is
+<code><a href='http://www.rdocumentation.org/packages/BiocParallel/topics/SerialParam-class'>SerialParam</a></code> which uses a single core.</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>additional arguments passes to <code><a href='http://www.rdocumentation.org/packages/zinbwave/topics/zinbFit'>zinbFit</a></code>.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>ZINBParams object containing the estimated parameters.</p>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>The function is a wrapper around <code><a href='http://www.rdocumentation.org/packages/zinbwave/topics/zinbFit'>zinbFit</a></code> that takes
+the fitted model and inserts it into a <code><a href='ZINBParams.html'>ZINBParams</a></code> object. See
+<code><a href='ZINBParams.html'>ZINBParams</a></code> for more details on the parameters and
+<code><a href='http://www.rdocumentation.org/packages/zinbwave/topics/zinbFit'>zinbFit</a></code> for details of the estimation procedure.</p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><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'>zinbEstimate</span>(<span class='no'>sc_example_counts</span>)</div><div class='output co'>#> <span class='message'>Removing all zero genes...</span></div><div class='output co'>#> <span class='message'>Fitting model...</span></div><div class='output co'>#> <span class='message'>Create model:</span></div><div class='output co'>#> <span class='message'>ok</span></div><div class='output co'>#> <span class='message'>Initialize parameters:</span></div><div class='output co'>#> <span class='message'>ok</span></div><div class='output co'>#> <span class='message'>Optimize parameters:</span></div><div class='output co'>#> <span class='message'>Iteration 1</span></div><div class='output co'>#> <span class='message'>penalized log-likelihood = -451653.610681949</span></div><div class='output co'>#> <span class='message'>After dispersion optimization = -451653.610681949</span></div><div class='output co'>#> user system elapsed
+#> 8.840 0.506 9.391 </div><div class='output co'>#> <span class='message'>After right optimization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>After orthogonalization = -451653.610681949</span></div><div class='output co'>#> user system elapsed
+#> 0.573 0.041 0.617 </div><div class='output co'>#> <span class='message'>After left optimization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>After orthogonalization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>Iteration 2</span></div><div class='output co'>#> <span class='message'>penalized log-likelihood = -200962.486229372</span></div><div class='output co'>#> <span class='message'>After dispersion optimization = -451653.610681949</span></div><div class='output co'>#> user system elapsed
+#> 6.414 0.345 6.790 </div><div class='output co'>#> <span class='message'>After right optimization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>After orthogonalization = -451653.610681949</span></div><div class='output co'>#> user system elapsed
+#> 0.616 0.025 0.643 </div><div class='output co'>#> <span class='message'>After left optimization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>After orthogonalization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>Iteration 3</span></div><div class='output co'>#> <span class='message'>penalized log-likelihood = -196682.271688862</span></div><div class='output co'>#> <span class='message'>After dispersion optimization = -451653.610681949</span></div><div class='output co'>#> user system elapsed
+#> 5.893 0.319 6.260 </div><div class='output co'>#> <span class='message'>After right optimization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>After orthogonalization = -451653.610681949</span></div><div class='output co'>#> user system elapsed
+#> 0.616 0.022 0.640 </div><div class='output co'>#> <span class='message'>After left optimization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>After orthogonalization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>Iteration 4</span></div><div class='output co'>#> <span class='message'>penalized log-likelihood = -195719.09604664</span></div><div class='output co'>#> <span class='message'>After dispersion optimization = -451653.610681949</span></div><div class='output co'>#> user system elapsed
+#> 4.808 0.251 5.075 </div><div class='output co'>#> <span class='message'>After right optimization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>After orthogonalization = -451653.610681949</span></div><div class='output co'>#> user system elapsed
+#> 0.600 0.013 0.615 </div><div class='output co'>#> <span class='message'>After left optimization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>After orthogonalization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>Iteration 5</span></div><div class='output co'>#> <span class='message'>penalized log-likelihood = -195487.316905869</span></div><div class='output co'>#> <span class='message'>After dispersion optimization = -451653.610681949</span></div><div class='output co'>#> user system elapsed
+#> 4.661 0.251 4.938 </div><div class='output co'>#> <span class='message'>After right optimization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>After orthogonalization = -451653.610681949</span></div><div class='output co'>#> user system elapsed
+#> 0.613 0.021 0.636 </div><div class='output co'>#> <span class='message'>After left optimization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>After orthogonalization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>Iteration 6</span></div><div class='output co'>#> <span class='message'>penalized log-likelihood = -195438.512431125</span></div><div class='output co'>#> <span class='message'>After dispersion optimization = -451653.610681949</span></div><div class='output co'>#> user system elapsed
+#> 4.363 0.219 4.594 </div><div class='output co'>#> <span class='message'>After right optimization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>After orthogonalization = -451653.610681949</span></div><div class='output co'>#> user system elapsed
+#> 0.520 0.019 0.540 </div><div class='output co'>#> <span class='message'>After left optimization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>After orthogonalization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>Iteration 7</span></div><div class='output co'>#> <span class='message'>penalized log-likelihood = -195429.243799278</span></div><div class='output co'>#> <span class='message'>ok</span></div><div class='input'><span class='no'>params</span></div><div class='output co'>#> A Params object of class ZINBParams
+#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'.
+#>
+#> Global:
+#> (GENES) (CELLS) [Seed]
+#> 1973 40 80751
+#>
+#> 1 additional parameters
+#>
+#> Model:
+#> ZinbModel with 1973 features, 40 samples, 0 latent factors and 4027 parameters
+#>
+#> Model Design:
+#> (SAMPLES) (GENES)
+#> 1, 1, 1, 1,... 1, 1, 1, 1,...
+#>
+#> Model Offsets:
+#> (MU) (PI)
+#> 40 x 1973 matrix 40 x 1973 matrix
+#>
+#> Model Indices:
+#> (Sample Mu) (Gene Mu) (Sample Pi) (Gene Pi)
+#> 1 1 1 1
+#>
+#> Model Intercepts:
+#> (Sample Mu) (Gene Mu) (Sample Pi) (Gene Pi)
+#> TRUE TRUE TRUE TRUE
+#>
+#> Model Latent factors:
+#> (W)
+#> 40 x 0 matrix
+#>
+#> Model Coefficients:
+#> (SAMPLE MU)
+#> 2.92563256904469, 2.4987993436997, 2.58202880827954, 1.97900548945704,...
+#> (GENE MU)
+#> 3.47522026895399, 2.47301357124798, 3.24285373024315, 3.18809031726884,...
+#> (Latent Mu)
+#> 0 x 1973 matrix
+#> (SAMPLE PI)
+#> -0.71252392787508, -2.22126441075684, -0.171737848601069, -1.44324267217097,...
+#> (GENE PI)
+#> -0.0394934045621859, 0.702003614655306, 0.522586914345766, 0.331946546846606,...
+#> (Latent Pi)
+#> 0 x 1973 matrix
+#>
+#> Model Regularisation:
+#> (Sample Mu) (GENE MU) (Sample Pi) (GENE PI)
+#> 1 49.325 1 49.325
+#> (LATENT) (Latent coeffs) (ZETA) (Logit)
+#> 49.325 1 1973 0.001
+#> </div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#details">Details</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
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diff --git a/docs/reference/zinbSimulate.html b/docs/reference/zinbSimulate.html
new file mode 100644
index 0000000000000000000000000000000000000000..2dea5b285307787c5c4a91773dfe5dbc2375b805
--- /dev/null
+++ b/docs/reference/zinbSimulate.html
@@ -0,0 +1,186 @@
+<!-- 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">
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+<title>ZINB-WaVE simulation — zinbSimulate • Splatter</title>
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+ <h1>ZINB-WaVE simulation</h1>
+ </div>
+
+
+ <p>Simulate counts using the ZINB-WaVE method.</p>
+
+
+ <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>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>params</th>
+ <td><p>ZINBParams object containing simulation parameters.</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>logical. Whether to print progress messages</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>any additional parameter settings to override what is provided in
+<code>params</code>.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SingleCellExperiment containing simulated counts</p>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>This function is just a wrapper around <code><a href='http://www.rdocumentation.org/packages/zinbwave/topics/zinbSim'>zinbSim</a></code> that
+takes a <code><a href='ZINBParams.html'>ZINBParams</a></code>, runs the simulation then converts the
+output to a <code><a href='http://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object.
+See <code><a href='http://www.rdocumentation.org/packages/zinbwave/topics/zinbSim'>zinbSim</a></code> and the ZINB-WaVE paper for
+more details about how the simulation works.</p>
+
+ <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+ <p>Campbell K, Yau C. Uncovering genomic trajectories with heterogeneous genetic
+and environmental backgrounds across single-cells and populations. bioRxiv
+(2017).</p>
+<p>Risso D, Perraudeau F, Gribkova S, Dudoit S, Vert J-P. ZINB-WaVE: A general
+and flexible method for signal extraction from single-cell RNA-seq data
+bioRxiv (2017).</p>
+<p>Paper: <a href='10.1101/125112'>10.1101/125112</a></p>
+<p>Code: <a href='https://github.com/drisso/zinbwave'>https://github.com/drisso/zinbwave</a></p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>zinbSimulate</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'>
+</div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#details">Details</a></li>
+
+ <li><a href="#references">References</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
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diff --git a/tests/testthat/test-ZINBParams.R b/tests/testthat/test-ZINBParams.R
index 4a4cfdece7ffc70332b918b9e87bd0c1c885eb8c..bbb7abd371aa1cddae7f7332201fe10bfc209f62 100644
--- a/tests/testthat/test-ZINBParams.R
+++ b/tests/testthat/test-ZINBParams.R
@@ -9,5 +9,5 @@ test_that("nGenes checks work", {
expect_error(setParam(params, "nGenes", 1),
"nGenes cannot be set directly")
expect_error(setParam(params, "nCells", 1),
- "nGenes cannot be set directly")
+ "nCells cannot be set directly")
})