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comparison report_clonality/RScript.r @ 66:7696dd687f39 draft

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author davidvanzessen
date Thu, 19 May 2016 09:42:53 -0400
parents 55f18bf19d72
children 69a6bba9ada9
comparison
equal deleted inserted replaced
65:5eaead0a68c5 66:7696dd687f39
577 samples = unique(clonalFreq$Sample) 577 samples = unique(clonalFreq$Sample)
578 for(sample in samples){ 578 for(sample in samples){
579 clonalFreqSample = clonalFreq[clonalFreq$Sample == sample,] 579 clonalFreqSample = clonalFreq[clonalFreq$Sample == sample,]
580 if(max(clonalFreqSample$Type) > 1){ 580 if(max(clonalFreqSample$Type) > 1){
581 for(i in 2:max(clonalFreqSample$Type)){ 581 for(i in 2:max(clonalFreqSample$Type)){
582 clonalFreqSample = clonalFreqSample[clonalFreqSample$Type == i,] 582 clonalFreqSampleType = clonalFreqSample[clonalFreqSample$Type == i,]
583 print(clonalFreqSample[clonalFreqSample$Type == i,]) 583 clonalityFrame.sub = clonalityFrame[clonalityFrame$clonaltype %in% clonalFreqSampleType$clonaltype,]
584 PRODF.sub = PRODF[PRODF$clonaltype %in% clonalFreqSample$clonaltype,] 584 clonalityFrame.sub = clonalityFrame.sub[order(clonalityFrame.sub$clonaltype),]
585 PRODF.sub = PRODF.sub[order(PRODF.sub$clonaltype),] 585 write.table(clonalityFrame.sub, file=paste("coincidences_", sample, "_", i, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
586 write.table(PRODF.sub, file=paste("coincidences_", sample, "_", i, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
587 } 586 }
588 } 587 }
589 } 588 }
590 589
591 clonalFreqCount = data.frame(data.table(clonalFreq)[, list(Count=.N), by=c("Sample", "Type")]) 590 clonalFreqCount = data.frame(data.table(clonalFreq)[, list(Count=.N), by=c("Sample", "Type")])
642 clonalityOverview = clonalFreqCount[c("Sample", "Type", "Count", "Weight", "WeightedCount")] 641 clonalityOverview = clonalFreqCount[c("Sample", "Type", "Count", "Weight", "WeightedCount")]
643 642
644 643
645 644
646 ClonalityOverviewPrint <- function(dat){ 645 ClonalityOverviewPrint <- function(dat){
646 dat = dat[order(dat[,2]),]
647 write.table(dat[-1], paste("ClonalityOverView_", unique(dat[1])[1,1] , ".csv", sep=""), sep=",",quote=F,na="-",row.names=F,col.names=F) 647 write.table(dat[-1], paste("ClonalityOverView_", unique(dat[1])[1,1] , ".csv", sep=""), sep=",",quote=F,na="-",row.names=F,col.names=F)
648 } 648 }
649 649
650 clonalityOverviewSplit = split(clonalityOverview, f=clonalityOverview$Sample) 650 clonalityOverviewSplit = split(clonalityOverview, f=clonalityOverview$Sample)
651 lapply(clonalityOverviewSplit, FUN=ClonalityOverviewPrint) 651 lapply(clonalityOverviewSplit, FUN=ClonalityOverviewPrint)