--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/deseq/differential_expression_analysis_pipeline_for_rnaseq_data-a03838a6eb54/DiffExpAnal/DESeqTools/exportDiff.R	Mon May 13 10:06:30 2013 -0400
@@ -0,0 +1,42 @@
+# exportDiff
+# export differentially expressed genes
+
+# input : complete, alpha, adjMethod, projectName
+# output : diff genes, up and down in xls files
+
+# created Feb 14th, 2012
+# Marie-Anges Dillies
+
+exportDiff <- function( complete, alpha, adjMethod, OUT_upName, OUT_downName, out = T ){
+	
+	diff <- complete[which(complete[,grep("adjp",colnames(complete))] < alpha),]
+
+	gup <- up( diff )	
+	gdown <- down( diff )
+	
+  if (out){
+    gup[,(ncol(gup)-4):ncol(gup)] <- format( gup[,(ncol(gup)-4):ncol(gup)], digits=3, dec=",")
+    gdown[,(ncol(gdown)-4):ncol(gdown)] <- format( gdown[,(ncol(gdown)-4):ncol(gdown)], digits=3, dec=",")
+		write.table(gup, file=OUT_upName, row.names=F, sep="\t")
+		write.table(gdown, file=OUT_downName, row.names=F, sep="\t")
+  }	
+  return( diff )
+}
+
+
+up <- function( diff ){
+		
+	up <- diff[diff$log2FC > 0,]
+	up <- up[order(up[,grep("adjp",colnames(up))]),]
+
+	return( up )	
+}
+
+
+down <- function( diff ){
+		
+	down <- diff[diff$log2FC < 0,]
+	down <- down[order(down[,grep("adjp",colnames(down))]),]
+
+	return( down )	
+}