--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/deseq/differential_expression_analysis_pipeline_for_rnaseq_data-a03838a6eb54/DiffExpAnal/DESeqTools/loadCountData.R	Mon May 13 10:06:30 2013 -0400
@@ -0,0 +1,36 @@
+# loadCountData
+# loads counts, one file per lane
+# file names from target file
+
+# input : target
+# output : raw count table
+
+# created Feb 6th, 2012
+# modified May 2nd, 2012 (colnames -> target$label)
+# Marie-Agnes Dillies
+
+
+loadCountData <- function(target, header){
+
+  require(DESeq)
+  fileNames <- target$files
+
+if(header!=0){
+	#rawCounts <- read.table(as.character(paste(rawDir,target$files[1],sep="/")), sep="\t", header=TRUE)
+	rawCounts <- read.table(as.character(target$files[1],sep="/"), sep="\t", header=TRUE)
+} else if(header==0){
+	rawCounts <- read.table(as.character(target$files[1],sep="/"), sep="\t")}
+  
+  colnames(rawCounts) <- c("Id", as.character(target$label[1]))
+
+  for (i in 2:length(fileNames)){
+	if(header!=0){
+  		tmp <- read.table(as.character(target$files[i],sep="/"), sep="\t", header=TRUE)
+	} else if(header==0){
+		tmp <- read.table(as.character(target$files[i],sep="/"), sep="\t")}
+  	colnames(tmp) <- c("Id", as.character(target$label[i]))
+  	rawCounts <- merge(rawCounts, tmp, by="Id", all=T)
+  }
+  rawCounts[is.na(rawCounts)] <- 0
+  return(rawCounts)
+}