v1.2.0

PF2-pasteur-fr · Dec 3, 2015 · 91e4586 · 91e4586
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,10 +2,10 @@ Package: SARTools
 Type: Package
 Title: Statistical Analysis of RNA-Seq Tools
 Version: 1.2.0
-Date: 2015-12-01
+Date: 2015-12-03
 Author: Marie-Agnes Dillies and Hugo Varet
 Maintainer: Hugo Varet <hugo.varet@pasteur.fr>
-Depends: R (>= 3.1.0), DESeq2 (>= 1.6.0), edgeR (>= 3.8.0), xtable
+Depends: R (>= 3.2.2), DESeq2 (>= 1.10.0), edgeR (>= 3.12.0), xtable
 Imports: knitr, GenomicRanges, S4Vectors, limma, genefilter (>= 1.44.0)
 VignetteBuilder: knitr
 Encoding: latin1

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,5 +1,3 @@
-# Generated by roxygen2 (4.1.1): do not edit by hand
-
 exportPattern("^[a-zA-Z]")
 import(DESeq2)
 import(edgeR)
@@ -10,3 +8,4 @@ importFrom(S4Vectors,mcols)
 importFrom(genefilter,shorth)
 importFrom(knitr,knit2html)
 importFrom(limma,plotMDS)
+importFrom(S4Vectors,metadata)
diff --git a/NEWS b/NEWS
@@ -6,6 +6,8 @@ CHANGES IN VERSION 1.2.0
 	o Fixed a bug when selecting the most variant features in PCAPlot()
 	o Fixed a bug when setting cpmCutoff to 0 using the edgeR script
 	o Vignette name is now "SARTools" instead of "tutorial"
+	o Mofidied the way of getting the independent filtering threshold (bug due to new DESeq2 version)
+	o New versions of R (3.2.2), DESeq2 (1.10.0) and edgeR (3.12.0) required
 
 CHANGES IN VERSION 1.1.0
 ------------------------

diff --git a/R/diagSizeFactorsPlots.R b/R/diagSizeFactorsPlots.R
@@ -4,32 +4,38 @@
 #'
 #' @param dds a \code{DESeqDataSet} object
 #' @param outfile TRUE to export the figure in a png file
+#' @param plots vector of plots to generate
 #' @return Two files in the figures directory: diagSizeFactorsHist.png containing one histogram per sample and diagSizeFactorsTC.png for a plot of the size factors vs the total number of reads
 #' @author Marie-Agnes Dillies and Hugo Varet
 
-diagSizeFactorsPlots <- function(dds, outfile=TRUE){
+diagSizeFactorsPlots <- function(dds, outfile=TRUE, plots=c("diag","sf_libsize")){
   # histograms
-  nrow <- ceiling(sqrt(ncol(counts(dds))))
-  ncol <- ceiling(ncol(counts(dds))/nrow)
-  if (outfile) png(filename="figures/diagSizeFactorsHist.png", width=300*max(ncol,nrow), height=300*min(ncol,nrow))
+  if ("diag" %in% plots){
+    nrow <- ceiling(sqrt(ncol(counts(dds))))
+    ncol <- ceiling(ncol(counts(dds))/nrow)
+    if (outfile) png(filename="figures/diagSizeFactorsHist.png", width=300*max(ncol,nrow), height=300*min(ncol,nrow))
     par(mfrow=sort(c(nrow,ncol)))
-	geomeans <- exp(rowMeans(log(counts(dds))))
+    geomeans <- exp(rowMeans(log(counts(dds))))
     samples <- colnames(counts(dds))
     counts.trans <- log2(counts(dds)/geomeans)
     xmin <- min(counts.trans[is.finite(counts.trans)],na.rm=TRUE)
     xmax <- max(counts.trans[is.finite(counts.trans)],na.rm=TRUE)
     for (j in 1:ncol(dds)){
-  	  hist(log2(counts(dds)[,j]/geomeans), nclass=100, xlab=expression(log[2] ~ (counts/geometric~mean)), las=1, xlim=c(xmin,xmax),
+      hist(log2(counts(dds)[,j]/geomeans), nclass=100, xlab=expression(log[2] ~ (counts/geometric~mean)), las=1, xlim=c(xmin,xmax),
            main=paste0("Size factors diagnostic - Sample ",samples[j]),col="skyblue")
       abline(v = log2(sizeFactors(dds)[j]), col="red", lwd=1.5)
     }
-  if (outfile) dev.off()
+    if (outfile) dev.off()
+  }
+
   # total read counts vs size factors
-  if (outfile) png(filename="figures/diagSizeFactorsTC.png",width=400,height=400)  
-	plot(sizeFactors(dds), colSums(counts(dds)), pch=19, las=1, xlab="Size factors",
-	     ylab="Total number of reads",main="Diagnostic: size factors vs total number of reads")
-	abline(lm(colSums(counts(dds)) ~ sizeFactors(dds) + 0), lty=2, col="grey")
-  if (outfile) dev.off()
+  if ("sf_libsize" %in% plots){
+    if (outfile) png(filename="figures/diagSizeFactorsTC.png",width=400,height=400)  
+    plot(sizeFactors(dds), colSums(counts(dds)), pch=19, las=1, xlab="Size factors",
+	 ylab="Total number of reads",main="Diagnostic: size factors vs total number of reads")
+    abline(lm(colSums(counts(dds)) ~ sizeFactors(dds) + 0), lty=2, col="grey")
+    if (outfile) dev.off()
+  }
 }
 
 
diff --git a/R/tabIndepFiltering.R b/R/tabIndepFiltering.R
@@ -9,7 +9,7 @@
 tabIndepFiltering <- function(results){
   out <- matrix(NA,ncol=3,nrow=length(names(results)),dimnames=list(names(results),c("Test vs Ref","Threshold","# discarded")))
   for (name in names(results)){
-	  threshold <- attr(results[[name]],"filterThreshold")
+	  threshold <- metadata(results[[name]])$filterThreshold
 	  out[name,2] <- round(threshold,2)
     use <- results[[name]]$baseMean > threshold
 	  out[name,3] <- ifelse(is.na(table(use)["FALSE"]),0,table(use)["FALSE"])

diff --git a/README.md b/README.md
@@ -8,7 +8,7 @@ SARTools is distributed with two R script templates (`template_script_DESeq2.r`
 How to install SARTools?
 ------------------------
 
-In addition to the SARTools package itself, the workflow requires the installation of several packages: DESeq2, edgeR, genefilter, xtable and knitr (all available online, see the dedicated webpages). SARTools needs R version 3.1.0 or higher, DESeq2 1.6.0 or higher and edgeR 3.8.5 or higher: old versions of DESeq2 or edgeR may be incompatible with SARTools.
+In addition to the SARTools package itself, the workflow requires the installation of several packages: DESeq2, edgeR, genefilter, xtable and knitr (all available online, see the dedicated webpages). SARTools needs R version 3.2.2 or higher, DESeq2 1.10.0 or higher and edgeR 3.12.0 or higher: old versions of DESeq2 or edgeR may be incompatible with SARTools.
 
 To install the SARTools package from GitHub, open a R session and:
 - install DESeq2, edgeR and genefilter with `source("http://bioconductor.org/biocLite.R")` and `biocLite(c("DESeq2", "edgeR", "genefilter"))` (if not installed yet)

diff --git a/inst/report_edgeR.rmd b/inst/report_edgeR.rmd
@@ -160,7 +160,7 @@ Normalization aims at correcting systematic technical biases in the data, in ord
 edgeR computes a factor for each sample. These normalization factors apply to the total number of counts and cannot be used to normalize read counts in a direct manner. Indeed, normalization factors are used to normalize total counts. These in turn are used to normalize read counts according to a total count normalization: if $N_j$ is the total number of reads of the sample $j$ and $f_j$ its normalization factor, $N'_j=f_j \times N_j$ is the normalized total number of reads. Then, let $s_j=N'_j/\bar{N'}$ with $\bar{N'}$ the mean of the $N'_j$ s. Finally, the normalized counts of the sample $j$ are defined as $x'_{ij}=x_{ij}/s_j$ where $i$ is the gene index.
 
 ```{r , cache=TRUE, echo=FALSE, results="asis"}
-print(xtable(t(matrix(out.edgeR$dge$samples$norm.factors, dimnames=list(target$label,"TMM"))),caption="Table 5: Normalization factors."), type="html", html.table.attributes = "align='center'")
+print(xtable(t(matrix(out.edgeR$dge$samples$norm.factors, dimnames=list(target$label,paste0(normalizationMethod," normalization factors")))),caption="Table 5: Normalization factors."), type="html", html.table.attributes = "align='center'")
 ```
 
 Boxplots are often used to assess the quality of the normalization process, as they show how distributions are globally affected during this process. We expect normalization to stabilize distributions across samples. Figure 8 shows boxplots of raw (left) and normalized (right) data respectively.

diff --git a/man/BCVPlot.Rd b/man/BCVPlot.Rd
diff --git a/man/MAPlot.Rd b/man/MAPlot.Rd
diff --git a/man/MDSPlot.Rd b/man/MDSPlot.Rd
diff --git a/man/PCAPlot.Rd b/man/PCAPlot.Rd
diff --git a/man/SARTools-package.Rd b/man/SARTools-package.Rd
diff --git a/man/SERE.Rd b/man/SERE.Rd
diff --git a/man/barplotNull.Rd b/man/barplotNull.Rd
diff --git a/man/barplotTotal.Rd b/man/barplotTotal.Rd
diff --git a/man/checkParameters.DESeq2.Rd b/man/checkParameters.DESeq2.Rd
diff --git a/man/checkParameters.edgeR.Rd b/man/checkParameters.edgeR.Rd
diff --git a/man/clusterPlot.Rd b/man/clusterPlot.Rd
diff --git a/man/countsBoxplots.Rd b/man/countsBoxplots.Rd
diff --git a/man/densityPlot.Rd b/man/densityPlot.Rd
diff --git a/man/descriptionPlots.Rd b/man/descriptionPlots.Rd
diff --git a/man/diagSizeFactorsPlots.Rd b/man/diagSizeFactorsPlots.Rd
diff --git a/man/dispersionsPlot.Rd b/man/dispersionsPlot.Rd
diff --git a/man/exploreCounts.Rd b/man/exploreCounts.Rd
diff --git a/man/exportResults.DESeq2.Rd b/man/exportResults.DESeq2.Rd
diff --git a/man/exportResults.edgeR.Rd b/man/exportResults.edgeR.Rd
diff --git a/man/loadCountData.Rd b/man/loadCountData.Rd
diff --git a/man/loadTargetFile.Rd b/man/loadTargetFile.Rd
diff --git a/man/majSequences.Rd b/man/majSequences.Rd
diff --git a/man/nDiffTotal.Rd b/man/nDiffTotal.Rd
diff --git a/man/pairwiseScatterPlots.Rd b/man/pairwiseScatterPlots.Rd
diff --git a/man/rawpHist.Rd b/man/rawpHist.Rd
diff --git a/man/removeNull.Rd b/man/removeNull.Rd
diff --git a/man/run.DESeq2.Rd b/man/run.DESeq2.Rd
diff --git a/man/run.edgeR.Rd b/man/run.edgeR.Rd
diff --git a/man/summarizeResults.DESeq2.Rd b/man/summarizeResults.DESeq2.Rd
diff --git a/man/summarizeResults.edgeR.Rd b/man/summarizeResults.edgeR.Rd
diff --git a/man/tabIndepFiltering.Rd b/man/tabIndepFiltering.Rd
diff --git a/man/tabSERE.Rd b/man/tabSERE.Rd
diff --git a/man/volcanoPlot.Rd b/man/volcanoPlot.Rd
diff --git a/man/writeReport.DESeq2.Rd b/man/writeReport.DESeq2.Rd
diff --git a/man/writeReport.edgeR.Rd b/man/writeReport.edgeR.Rd
diff --git a/template_script_DESeq2.r b/template_script_DESeq2.r
@@ -2,7 +2,7 @@
 ### R script to compare several conditions with the SARTools and DESeq2 packages
 ### Hugo Varet
 ### April 20th, 2015
-### designed to be executed with SARTools 1.1.1
+### designed to be executed with SARTools 1.2.0
 ################################################################################
 
 ################################################################################

diff --git a/template_script_edgeR.r b/template_script_edgeR.r
@@ -2,7 +2,7 @@
 ### R script to compare several conditions with the SARTools and edgeR packages
 ### Hugo Varet
 ### April 20th, 2015
-### designed to be executed with SARTools 1.1.1
+### designed to be executed with SARTools 1.2.0
 ################################################################################
 
 ################################################################################

diff --git a/vignettes/SARTools.rmd b/vignettes/SARTools.rmd
@@ -202,7 +202,7 @@ targetFile <- system.file("target.txt", package="SARTools")
 rawDir <- system.file("raw", package="SARTools")
 ```
 
-The user can try the R scripts `template_script_DESeq2.r` and `template_script_edgeR.r` with the parameters above (all the others remaining unchanged).
+The user can try the R scripts `template_script_DESeq2.r` and `template_script_edgeR.r` specifying a working directory (`workDir`) and with the parameters above (all the others remaining unchanged).
 
 ## Bibliography