Mercurial > repos > sblanck > mpagenomics_normalize

annotate filter.R @ 6:7dc6ce39fb89 default tip

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add selection tool
author blanck
date Wed, 29 Apr 2015 10:08:52 +0200
parents b7f3854e08f8
children
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1 args<-commandArgs(TRUE)
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3 input=args[1]
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4 length=as.numeric(args[2])
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5 probes=as.numeric(args[3])
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6 tmp_dir=args[4]
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7 nbcall=as.vector(args[5])
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8 output=args[6]
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10 nbcall_tmp <- strsplit(nbcall,",")
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11 nbcall_vecstring <-unlist(nbcall_tmp)
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13 nbcall_vecstring
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15 library(MPAgenomics)
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16 workdir=file.path(tmp_dir, "mpagenomics")
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17 setwd(workdir)
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19 segcall = read.table(input, header = TRUE)
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20 filtercall=filterSeg(segcall,length,probes,nbcall_vecstring)
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21 sink(output)
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22 print(format(filtercall),row.names=FALSE)
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23 sink()
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24 #write.table(filtercall,output,row.names = FALSE, quote = FALSE, sep = "\t")
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