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comparison 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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9:a03838a6eb54 10:6e573fd3c41b
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 }