--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/DiffExpAnal/DESeqTools/HTseqClean.R	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,19 @@
+# HTseqClean
+# remove extra counts out of genes
+# for HTseq output
+
+# input : rawCounts
+# output : cleaned rawCounts
+
+# created Feb 6th, 2012
+# Modified Feb 16th, 2012
+# Marie-Agnes Dillies
+
+
+HTseqClean <- function( rawCounts ){
+
+  row2remove <- c("alignment_not_unique", "ambiguous", "no_feature", "not_aligned", "too_low_aQual")
+  rawCounts <- rawCounts[!rawCounts$Id %in% row2remove,]
+  rawCounts[is.na(rawCounts)] <- 0
+  return(rawCounts)
+}