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annotate SMART/DiffExpAnal/DESeqTools/HTseqClean.R @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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1 # HTseqClean
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2 # remove extra counts out of genes
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3 # for HTseq output
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4
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5 # input : rawCounts
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6 # output : cleaned rawCounts
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7
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8 # created Feb 6th, 2012
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9 # Modified Feb 16th, 2012
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10 # Marie-Agnes Dillies
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13 HTseqClean <- function( rawCounts ){
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14
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15 row2remove <- c("alignment_not_unique", "ambiguous", "no_feature", "not_aligned", "too_low_aQual")
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16 rawCounts <- rawCounts[!rawCounts$Id %in% row2remove,]
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17 rawCounts[is.na(rawCounts)] <- 0
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18 return(rawCounts)
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19 }