Mercurial > repos > yufei-luo > differential_expression_analysis_pipeline_for_rnaseq_data

diff deseq/differential_expression_analysis_pipeline_for_rnaseq_data-a03838a6eb54/DiffExpAnal/DESeqTools/HTseqClean.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/HTseqClean.R	Mon May 13 10:06:30 2013 -0400
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+# 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)
+}