Mercurial > repos > yufei-luo > differential_expression_analysis_pipeline_for_rnaseq_data

diff deseq/differential_expression_analysis_pipeline_for_rnaseq_data-a03838a6eb54/DiffExpAnal/DESeqTools/exportComplete.R @ 10:6e573fd3c41b draft

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author yufei-luo
date Mon, 13 May 2013 10:06:30 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/deseq/differential_expression_analysis_pipeline_for_rnaseq_data-a03838a6eb54/DiffExpAnal/DESeqTools/exportComplete.R	Mon May 13 10:06:30 2013 -0400
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+# exportComplete
+# export complete data and results
+
+# input : counts res, target
+# output : complete data and xls file (in text format)
+
+# created Feb 14th, 2012
+# modified March 9th, 2012 (order of cond1 and cond2)
+# Marie-Anges Dillies
+
+exportComplete <- function( counts, res, target, adjMethod, cond1, cond2, OUT_completeName, out = T ){
+	
+	complete <- data.frame( res$id, counts, res[,3:ncol(res)] )
+	colnames(complete) <- c( "id", as.character(target$label), cond2, cond1, "FC", "log2FC", "rawp", 
+							paste("adjp",adjMethod,sep="") )
+
+  if (out)
+  		write.table( complete, file=OUT_completeName, sep="\t", row.names=F )
+  return( complete )
+}