Mercurial > repos > davidvanzessen > extract_duplicates

annotate extract_duplicates.r @ 1:a3c4e3e62e10 draft

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author davidvanzessen
date Tue, 01 Sep 2015 07:49:47 -0400
parents 02cf2dd19564
children 1f1640608245
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1 args <- commandArgs(trailingOnly = TRUE)
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3 input=args[1]
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4 column=as.numeric(args[2])
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5 header=(args[3] == "yes")
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6 out_file=args[4]
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8 dat = read.table(input, header=header, sep="\t", fill=T, stringsAsFactors=F, quote="")
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10 duplicates = dat[duplicated(dat[,column]),column]
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12 dat = dat[dat[,column] %in% duplicates,]
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14 dat = dat[order(dat[,column]),]
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16 write.table(dat, out_file, sep="\t", row.names=F, col.names=header, quote=F)