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1 args<-commandArgs(TRUE)
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2
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3 input=args[1]
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4 tmp_dir=args[2]
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5 nbcall=as.numeric(args[3])
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6 cellularity=as.numeric(args[4])
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7 output=args[5]
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8 method=args[6]
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9 userId=args[7]
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10 signalType=args[8]
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11
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12 library(MPAgenomics)
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13 workdir=file.path(tmp_dir, "mpagenomics",userId)
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14 setwd(workdir)
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15
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16 CN=read.table(input,header=TRUE)
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17 uniqueChr=unique(CN$chromosome)
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18 drops=c("chromosome","position","probeName")
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19 CNsignal=CN[,!(names(CN)%in% drops),drop=FALSE]
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20
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21 samples=names(CNsignal)
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22
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23 if (signalType=="CN")
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24 {
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25
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26 result=data.frame(sampleNames=character(0),chrom=character(0),chromStart=numeric(0),chromEnd=numeric(0),probes=numeric(0),means=numeric(0),calls=character(0),stringsAsFactors=FALSE)
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27
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28 for (chr in uniqueChr)
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29 {
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30 currentSubset=subset(CN, chromosome==chr)
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31 currentPositions=currentSubset["position"]
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32 for (sample in samples)
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33 {
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34 currentSignal=currentSubset[sample]
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35 if (length(which(!is.na(unlist(currentSignal))))>1)
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36 {
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37 currentSeg=segmentation(signal=unlist(currentSignal),position=unlist(currentPositions),method=method)
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38 callobj= callingObject(copynumber=currentSeg$signal, segmented=currentSeg$segmented,chromosome=rep(chr,length(currentSeg$signal)), position=currentSeg$startPos,sampleNames=sample)
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39 currentCall=callingProcess(callobj,nclass=nbcall,cellularity=cellularity,verbose=TRUE)
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40 currentResult=currentCall$segment
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41 currentResult["sampleNames"]=c(rep(sample,length(currentCall$segment$chrom)))
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42 result=rbind(result,currentResult)
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43 }
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44 }
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45 }
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46 finalResult=data.frame(sampleNames=result["sampleNames"],chrom=result["chrom"],chromStart=result["chromStart"],chromEnd=result["chromEnd"],probes=result["probes"],means=result["means"],calls=result["calls"],stringsAsFactors=FALSE)
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47 sink(output)
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48 print(format(finalResult))
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49 sink()
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50 #write.table(finalResult,output,row.names = FALSE, quote=FALSE, sep = "\t")
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51 } else {
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52 result=data.frame(sampleNames=character(0),chrom=character(0),start=numeric(0),end=numeric(0),points=numeric(0),means=numeric(0),stringsAsFactors=FALSE)
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53
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54 for (chr in uniqueChr)
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55 {
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56 cat(paste0("chromosome ",chr,"\n"))
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57 currentSubset=subset(CN, chromosome==chr)
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58 currentPositions=currentSubset["position"]
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59 for (sample in samples)
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60 {
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61 cat(paste0(" sample ",sample,"..."))
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62 currentSignal=currentSubset[sample]
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63 if (length(which(!is.na(unlist(currentSignal))))>1)
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64 {
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65 currentSeg=segmentation(signal=unlist(currentSignal),position=unlist(currentPositions),method=method)
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66 currentResult=currentSeg$segment
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67 currentResult["chrom"]=c(rep(chr,length(currentSeg$segment$means)))
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68 currentResult["sampleNames"]=c(rep(sample,length(currentSeg$segment$means)))
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69 result=rbind(result,currentResult)
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70
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71 }
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72 cat(paste0("OK\n"))
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73 }
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74 }
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75 finalResult=data.frame(sampleNames=result["sampleNames"],chrom=result["chrom"],chromStart=result["start"],chromEnd=result["end"],probes=result["points"],means=result["means"],stringsAsFactors=FALSE)
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76 sink(output)
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77 print(format(finalResult))
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78 sink()
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79 #write.table(finalResult,output,row.names = FALSE, quote=FALSE, sep = "\t")
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80 }
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81
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