Skip to content
Snippets Groups Projects
Commit 0188e6fe authored by l.zappia's avatar l.zappia
Browse files

Merge branch 'master' into devel

* master: (123 commits)
  Fix non-linear path factors
  Bump verison number
  Set some examples to not run to save check time
  Initalise scDatEx to avoid NOTE
  Tidy up and bump version
  Replace 1:x
  Remove splatter.Rproj
  Add more detail about counts matrix
  Add installation to vignette
  Set R_TESTS environment
  Bump version to start build
  splatter 0.99.3
  Updata scDDEstimate
  Add condition parameter
  Modify SCDDParams to take SummarizedExperiment
  Add logo to vignettes directory
  Remove scDD github remote
  Update to R-devel
  Address Bioconductor build warnings, notes
  Prepare for Bioconductor submission
  ...

From: Luke Zappia <lazappi@users.noreply.github.com>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@126081 bc3139a8-67e5-0310-9ffc-ced21a209358
parent 070784c4
No related branches found
No related tags found
No related merge requests found
Package: splatter Package: splatter
Type: Package Type: Package
Title: Simple Simulation of Single-cell RNA Sequencing Data Title: Simple Simulation of Single-cell RNA Sequencing Data
Version: 0.99.7 Version: 0.99.8
Date: 2016-12-29 Date: 2017-01-23
Author: Luke Zappia Author: Luke Zappia
Authors@R: c(person("Luke", "Zappia", role = c("aut", "cre"), email = Authors@R:
"luke.zappia@mcri.edu.au"), person("Belinda", "Phipson", role = c(person("Luke", "Zappia", role = c("aut", "cre"),
c("aut"), email = "belinda.phipson@mcri.edu.au"), email = "luke.zappia@mcri.edu.au"),
person("Alicia", "Oshlack", role = c("aut"), email = person("Belinda", "Phipson", role = c("aut"),
"alicia.oshlack@mcri.edu.au")) email = "belinda.phipson@mcri.edu.au"),
person("Alicia", "Oshlack", role = c("aut"),
email = "alicia.oshlack@mcri.edu.au"))
Maintainer: Luke Zappia <luke.zappia@mcri.edu.au> Maintainer: Luke Zappia <luke.zappia@mcri.edu.au>
Description: Splatter is a package for the simulation of single-cell Description: Splatter is a package for the simulation of single-cell RNA
RNA sequencing count data. It provides a simple interface for sequencing count data. It provides a simple interface for creating complex
creating complex simulations that are reproducible and simulations that are reproducible and well-documented.
well-documented.
License: GPL-3 + file LICENSE License: GPL-3 + file LICENSE
LazyData: TRUE LazyData: TRUE
Depends: R (>= 3.4), scater Depends:
Imports: fitdistrplus, edgeR, stats, locfit, akima, Biobase, checkmate, R (>= 3.4),
methods, utils, matrixStats, ggplot2, scales scater
Suggests: testthat, scran, progress, lme4, pscl, scDD, knitr, Imports:
rmarkdown, BiocStyle, covr, S4Vectors, SummarizedExperiment fitdistrplus,
biocViews: SingleCell, RNASeq, Transcriptomics, GeneExpression, edgeR,
Sequencing, Software stats,
locfit,
akima,
Biobase,
checkmate,
methods,
utils,
matrixStats,
ggplot2,
scales
Suggests:
testthat,
scran,
progress,
lme4,
pscl,
scDD,
knitr,
rmarkdown,
BiocStyle,
covr,
S4Vectors,
SummarizedExperiment
biocViews: SingleCell, RNASeq, Transcriptomics, GeneExpression, Sequencing,
Software
URL: https://github.com/Oshlack/splatter URL: https://github.com/Oshlack/splatter
BugReports: https://github.com/Oshlack/splatter/issues BugReports: https://github.com/Oshlack/splatter/issues
RoxygenNote: 5.0.1 RoxygenNote: 5.0.1
......
# 0.99.8
* Fix bug that meant non-linear path factors weren't stored in output
# 0.99.7 # 0.99.7
* Small changes to avoid NOTEs and reduce check time * Small changes to avoid NOTEs and reduce check time
......
...@@ -53,27 +53,29 @@ ...@@ -53,27 +53,29 @@
#' \describe{ #' \describe{
#' \item{Gene}{Unique gene identifier.} #' \item{Gene}{Unique gene identifier.}
#' \item{BaseGeneMean}{The base expression level for that gene.} #' \item{BaseGeneMean}{The base expression level for that gene.}
#' \item{OutlierFactor}{Expression outlier factor for that gene. Values #' \item{OutlierFactor}{Expression outlier factor for that gene.
#' of 1 indicate the gene is not an expression outlier.} #' Values of 1 indicate the gene is not an expression outlier.}
#' \item{GeneMean}{Expression level after applying outlier factors.} #' \item{GeneMean}{Expression level after applying outlier factors.}
#' \item{DEFac[Group]}{The differential expression factor for each gene #' \item{DEFac[Group]}{The differential expression factor for each
#' in a particular group. Values of 1 indicate the gene is not #' gene in a particular group. Values of 1 indicate the gene is not
#' differentially expressed.} #' differentially expressed.}
#' \item{GeneMean[Group]}{Expression level of a gene in a particular #' \item{GeneMean[Group]}{Expression level of a gene in a particular
#' group after applying differential expression factors.} #' group after applying differential expression factors.}
#' \item{SigmaFac[Path]}{Factor applied to genes that have
#' non-linear changes in expression along a path.}
#' } #' }
#' } #' }
#' \item{\code{assayData}}{ #' \item{\code{assayData}}{
#' \describe{ #' \describe{
#' \item{BaseCellMeans}{The expression of genes in each cell adjusted for #' \item{BaseCellMeans}{The expression of genes in each cell
#' expected library size.} #' adjusted for expected library size.}
#' \item{BCV}{The Biological Coefficient of Variation for each gene in #' \item{BCV}{The Biological Coefficient of Variation for each gene
#' each cell.} #' in each cell.}
#' \item{CellMeans}{The expression level of genes in each cell adjusted #' \item{CellMeans}{The expression level of genes in each cell
#' for BCV.} #' adjusted for BCV.}
#' \item{TrueCounts}{The simulated counts before dropout.} #' \item{TrueCounts}{The simulated counts before dropout.}
#' \item{Dropout}{Logical matrix showing which values have been dropped #' \item{Dropout}{Logical matrix showing which values have been
#' in which cells.} #' dropped in which cells.}
#' } #' }
#' } #' }
#' } #' }
...@@ -449,6 +451,15 @@ splatSimPathCellMeans <- function(sim, params) { ...@@ -449,6 +451,15 @@ splatSimPathCellMeans <- function(sim, params) {
group.names <- unique(groups) group.names <- unique(groups)
exp.lib.sizes <- pData(sim)$ExpLibSize exp.lib.sizes <- pData(sim)$ExpLibSize
# Generate non-linear path factors
for (idx in seq_along(path.from)) {
# Select genes to follow a non-linear path
is.nonlinear <- as.logical(rbinom(nGenes, 1, path.nonlinearProb))
sigma.facs <- rep(0, nGenes)
sigma.facs[is.nonlinear] <- path.sigmaFac
fData(sim)[[paste0("SigmaFacPath", idx)]] <- sigma.facs
}
# Generate paths. Each path is a matrix with path.length columns and # Generate paths. Each path is a matrix with path.length columns and
# nGenes rows where the expression from each genes changes along the path. # nGenes rows where the expression from each genes changes along the path.
path.steps <- lapply(seq_along(path.from), function(idx) { path.steps <- lapply(seq_along(path.from), function(idx) {
...@@ -462,16 +473,13 @@ splatSimPathCellMeans <- function(sim, params) { ...@@ -462,16 +473,13 @@ splatSimPathCellMeans <- function(sim, params) {
# Find the means at the end position # Find the means at the end position
means.end <- fData(sim)[[paste0("GeneMeanPath", idx)]] means.end <- fData(sim)[[paste0("GeneMeanPath", idx)]]
# Select genes to follow a non-linear path # Get the non-linear factors
is.nonlinear <- as.logical(rbinom(nGenes, 1, path.nonlinearProb)) sigma.facs <- fData(sim)[[paste0("SigmaFacPath", idx)]]
sigma.facs <- rep(0, nGenes)
sigma.facs[is.nonlinear] <- path.sigmaFac
# Build Brownian bridges from start to end # Build Brownian bridges from start to end
steps <- buildBridges(means.start, means.end, n = path.length[idx], steps <- buildBridges(means.start, means.end, n = path.length[idx],
sigma.fac = sigma.facs) sigma.fac = sigma.facs)
fData(sim)[[paste0("SigmaFacPath", idx)]] <- sigma.facs
return(t(steps)) return(t(steps))
}) })
......
...@@ -78,27 +78,29 @@ slots. This additional information includes: ...@@ -78,27 +78,29 @@ slots. This additional information includes:
\describe{ \describe{
\item{Gene}{Unique gene identifier.} \item{Gene}{Unique gene identifier.}
\item{BaseGeneMean}{The base expression level for that gene.} \item{BaseGeneMean}{The base expression level for that gene.}
\item{OutlierFactor}{Expression outlier factor for that gene. Values \item{OutlierFactor}{Expression outlier factor for that gene.
of 1 indicate the gene is not an expression outlier.} Values of 1 indicate the gene is not an expression outlier.}
\item{GeneMean}{Expression level after applying outlier factors.} \item{GeneMean}{Expression level after applying outlier factors.}
\item{DEFac[Group]}{The differential expression factor for each gene \item{DEFac[Group]}{The differential expression factor for each
in a particular group. Values of 1 indicate the gene is not gene in a particular group. Values of 1 indicate the gene is not
differentially expressed.} differentially expressed.}
\item{GeneMean[Group]}{Expression level of a gene in a particular \item{GeneMean[Group]}{Expression level of a gene in a particular
group after applying differential expression factors.} group after applying differential expression factors.}
\item{SigmaFac[Path]}{Factor applied to genes that have
non-linear changes in expression along a path.}
} }
} }
\item{\code{assayData}}{ \item{\code{assayData}}{
\describe{ \describe{
\item{BaseCellMeans}{The expression of genes in each cell adjusted for \item{BaseCellMeans}{The expression of genes in each cell
expected library size.} adjusted for expected library size.}
\item{BCV}{The Biological Coefficient of Variation for each gene in \item{BCV}{The Biological Coefficient of Variation for each gene
each cell.} in each cell.}
\item{CellMeans}{The expression level of genes in each cell adjusted \item{CellMeans}{The expression level of genes in each cell
for BCV.} adjusted for BCV.}
\item{TrueCounts}{The simulated counts before dropout.} \item{TrueCounts}{The simulated counts before dropout.}
\item{Dropout}{Logical matrix showing which values have been dropped \item{Dropout}{Logical matrix showing which values have been
in which cells.} dropped in which cells.}
} }
} }
} }
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment