Merge pull request #45 from PF2-pasteur-fr/development

Development
PF2-pasteur-fr · May 23, 2018 · b5fa8e8 · b5fa8e8
2 parents 4ddef16 + 2285f88
commit b5fa8e8
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Showing 7 changed files with 14 additions and 10 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: SARTools
 Type: Package
 Title: Statistical Analysis of RNA-Seq Tools
-Version: 1.6.1
-Date: 2018-03-20
+Version: 1.6.2
+Date: 2018-05-23
 Author: Marie-Agnes Dillies and Hugo Varet
 Maintainer: Hugo Varet <[email protected]>
 Depends: R (>= 3.3.0), DESeq2 (>= 1.12.0), edgeR (>= 3.12.0), xtable

diff --git a/NEWS b/NEWS
@@ -1,4 +1,8 @@
-CHANGES IN VERSION 1.6.1
+CHANGES IN VERSION 1.6.2
+------------------------
+	o fixed a bug in template_script_edgeR_CL.r to use forceCairoGraph option
+	o fixed a bug in loadCountData() function
+
 ------------------------
 	o new boolean parameter forceCairoGraph
 	o adapt size of PNG plots if width/height are too large

diff --git a/R/loadCountData.R b/R/loadCountData.R
@@ -41,7 +41,7 @@ loadCountData <- function(target, rawDir="raw", skip=0, featuresToRemove=c("alig
   cat(files[1],": ",length(rawCounts[,labels[1]])," rows and ",sum(rawCounts[,labels[1]]==0)," null count(s)\n",sep="")
 
   for (i in 2:length(files)){
-    tmp <- read.table(file.path(rawDir, files[i]), sep="\t", header=header, skip=skip, stringsAsFactors=FALSE)
+    tmp <- read.table(file.path(rawDir, files[i]), sep="\t", quote="\"", header=header, skip=skip, stringsAsFactors=FALSE)
     tmp <- tmp[,c(idCol, countsCol)]
     colnames(tmp) <- c("Id", labels[i])
     if (any(duplicated(tmp$Id))) stop("Duplicated feature names in ", files[i])

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
 ### March 20th, 2018
-### designed to be executed with SARTools 1.6.1
+### designed to be executed with SARTools 1.6.2
 ################################################################################
 
 ################################################################################

diff --git a/template_script_DESeq2_CL.r b/template_script_DESeq2_CL.r
@@ -2,7 +2,7 @@
 ### R script to compare several conditions with the SARTools and DESeq2 packages
 ### Hugo Varet
 ### March 20th, 2018
-### designed to be executed with SARTools 1.6.1
+### designed to be executed with SARTools 1.6.2
 ### run "Rscript template_script_DESeq2_CL.r --help" to get some help
 ################################################################################
 

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
 ### March 20th, 2018
-### designed to be executed with SARTools 1.6.1
+### designed to be executed with SARTools 1.6.2
 ################################################################################
 
 ################################################################################

diff --git a/template_script_edgeR_CL.r b/template_script_edgeR_CL.r
@@ -1,8 +1,8 @@
 ################################################################################
 ### R script to compare several conditions with the SARTools and edgeR packages
 ### Hugo Varet
-### March 20th, 2018
-### designed to be executed with SARTools 1.6.1
+### May 16th, 2018
+### designed to be executed with SARTools 1.6.2
 ### run "Rscript template_script_edgeR_CL.r --help" to get some help
 ################################################################################
 
@@ -81,7 +81,7 @@ make_option(c("-C", "--colors"),
 			dest="cols",
 			help="colors of each biological condition on the plots\n\t\t\"col1,col2,col3,col4\"\n\t\t[default: %default]"),
 
-make_option(c("-g", "--forceCairoGraph"),
+make_option(c("-f", "--forceCairoGraph"),
             action="store_true",
             default=FALSE,
             dest="forceCairoGraph",