Avoiding check.names while reading data. Thanks to Guillaume Noell fo…

…r the hint
adluchessi · Dec 18, 2017 · ad997df · ad997df
1 parent d484f69
commit ad997df
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Showing 3 changed files with 7 additions and 3 deletions.
diff --git a/lib/CbBio/RNASeq/R-Scripts/DE_EdgeR.R b/lib/CbBio/RNASeq/R-Scripts/DE_EdgeR.R
@@ -98,7 +98,9 @@ DE_EdgeR<-function(projectdir,dir,file,targetfile,label,contrastfile, filter, cp
   #Importing the data
   workingDir<-projectdir
   setwd(workingDir)
-  data <- read.table(file, header=TRUE, sep="\t")
+
+  #added check.names=F suggested by Guillaume Noell
+  data <- read.table(file, header=TRUE, sep="\t",check.names=F)
   data<-data[,sort(colnames(data))]
 
 

diff --git a/lib/CbBio/RNASeq/R-Scripts/DE_noiseq.R b/lib/CbBio/RNASeq/R-Scripts/DE_noiseq.R
@@ -85,7 +85,8 @@ DE_noiseq<-function(projectdir,dir,file,targetsfile,label,filter,contrastfile,le
   #Importing the data
   workingDir<-dir
   setwd(workingDir)
-  data<-read.table(file=file, sep="\t", header=T)
+  #added check.names=F suggested by Guillaume Noell
+  data<-read.table(file=file, sep="\t", header=T,check.names=F)
   #Checking any additional data provided to use in data exploration
   if(!missing(lenghtfile)){
     mylength<-read.table(file=lenghtfile, sep="\t", header=T)

diff --git a/lib/CbBio/RNASeq/R-Scripts/QC_EdgeR.R b/lib/CbBio/RNASeq/R-Scripts/QC_EdgeR.R
@@ -98,7 +98,8 @@ QC_EdgeR<-function(projectdir,dir,file,targetfile,label,filter, cpmvalue=1, rept
   workingDir<-dir
   setwd(workingDir)
   filepath<-file.path(workingDir,file)
-  data <- read.table(filepath, header=TRUE, sep="\t")
+  #added check.names=F suggested by Guillaume Noell
+  data <- read.table(filepath, header=TRUE, sep="\t",check.names=F)
 
   data<-data[,sort(colnames(data))]