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author yufei-luo
date Mon, 13 May 2013 10:06:30 -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)
}