Mercurial > repos > sblanck > mpagenomics_normalize
view segcall.R @ 6:7dc6ce39fb89 default tip
add selection tool
author | blanck |
---|---|
date | Wed, 29 Apr 2015 10:08:52 +0200 |
parents | b7f3854e08f8 |
children |
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args<-commandArgs(TRUE) chrom=args[1] dataset=args[2] output=args[3] tmp_dir=args[4] nbcall=as.numeric(args[5]) input=args[6] outputfigures=type.convert(args[7]) snp=type.convert(args[8]) tumorcsv=args[9] cellularity=as.numeric(args[10]) user=args[11] method=args[12] library(MPAgenomics) workdir=file.path(tmp_dir, "mpagenomics",user) setwd(workdir) if (grepl("all",tolower(chrom)) | chrom=="None") { chrom_vec=c(1:25) } else { chrom_tmp <- strsplit(chrom,",") chrom_vecstring <-unlist(chrom_tmp) chrom_vec <- as.numeric(chrom_vecstring) } input_tmp <- strsplit(input,",") input_tmp_vecstring <-unlist(input_tmp) input_vecstring = sub("^([^.]*).*", "\\1", input_tmp_vecstring) if (dataset == input) { if (tumorcsv== "none") { segcall=cnSegCallingProcess(dataset,chromosome=chrom_vec, nclass=nbcall, savePlot=outputfigures,onlySNP=snp, cellularity=cellularity, method=method) } else { segcall=cnSegCallingProcess(dataset,chromosome=chrom_vec, normalTumorArray=tumorcsv, nclass=nbcall, savePlot=outputfigures,onlySNP=snp, cellularity=cellularity, method=method) } } else { if (tumorcsv== "none") { segcall=cnSegCallingProcess(dataset,chromosome=chrom_vec, listOfFiles=input_vecstring, nclass=nbcall, savePlot=outputfigures, onlySNP=snp, cellularity=cellularity, method=method) } else { segcall=cnSegCallingProcess(dataset,chromosome=chrom_vec, normalTumorArray=tumorcsv, listOfFiles=input_vecstring, nclass=nbcall, savePlot=outputfigures, onlySNP=snp, cellularity=cellularity, method=method) } } sink(output) print(format(segcall)) sink() #write.table(format(segcall),output,row.names = FALSE, quote=FALSE, sep = "\t") #write.fwf(segcall,output,rownames = FALSE, quote=FALSE, sep = "\t") quit()