Mercurial > repos > yufei-luo > differential_expression_analysis_pipeline_for_rnaseq_data
annotate 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 |
| parents | |
| children |
| rev | line source |
|---|---|
| 10 | 1 # HTseqClean |
| 2 # remove extra counts out of genes | |
| 3 # for HTseq output | |
| 4 | |
| 5 # input : rawCounts | |
| 6 # output : cleaned rawCounts | |
| 7 | |
| 8 # created Feb 6th, 2012 | |
| 9 # Modified Feb 16th, 2012 | |
| 10 # Marie-Agnes Dillies | |
| 11 | |
| 12 | |
| 13 HTseqClean <- function( rawCounts ){ | |
| 14 | |
| 15 row2remove <- c("alignment_not_unique", "ambiguous", "no_feature", "not_aligned", "too_low_aQual") | |
| 16 rawCounts <- rawCounts[!rawCounts$Id %in% row2remove,] | |
| 17 rawCounts[is.na(rawCounts)] <- 0 | |
| 18 return(rawCounts) | |
| 19 } |