comparison RScript.r @ 3:e1aa99d86a8a draft

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2:1c5927d0a4ce

if("Replicate" %in% colnames(test))
{
	clonalityFrame = PROD
	clonalityFrame$ReplicateConcat = do.call(paste, c(clonalityFrame[c("VDJCDR3", "Sample", "Replicate")], sep = ":"))
	clonalityFrame = clonalityFrame[!duplicated(clonalityFrame$ReplicateConcat), ]
	clonalFreq = data.frame(data.table(clonalityFrame)[, list(Type=.N), by=c("Sample", "VDJCDR3")])
	clonalFreqCount = data.frame(data.table(clonalFreq)[, list(Count=.N), by=c("Sample", "Type")])
	clonalFreqCount$realCount = clonalFreqCount$Type * clonalFreqCount$Count
	clonalSum = data.frame(data.table(clonalFreqCount)[, list(Reads=sum(realCount)), by=c("Sample")])
	clonalFreqCount = merge(clonalFreqCount, clonalSum, by.x="Sample", by.y="Sample")

3:e1aa99d86a8a

if("Replicate" %in% colnames(test))
{
	clonalityFrame = PROD
	clonalityFrame$ReplicateConcat = do.call(paste, c(clonalityFrame[c("VDJCDR3", "Sample", "Replicate")], sep = ":"))
	clonalityFrame = clonalityFrame[!duplicated(clonalityFrame$ReplicateConcat), ]
	
	write.table(clonalityFrame, "clonalityComplete.tsv", sep="\t",quote=F,row.names=T,col.names=T)

	ClonalitySampleReplicatePrint <- function(dat){
	    write.table(dat, paste("clonality_", unique(dat$Sample) , "_", unique(dat$Replicate), ".tsv", sep=""), sep="\t",quote=F,row.names=T,col.names=T)
	}

    clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,c("Sample", "Replicate")])
    lapply(clonalityFrameSplit, FUN=ClonalitySampleReplicatePrint)

    ClonalitySamplePrint <- function(dat){
	    write.table(dat, paste("clonality_", unique(dat$Sample) , ".tsv", sep=""), sep="\t",quote=F,row.names=T,col.names=T)
	}

    clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,"Sample"])
    lapply(clonalityFrameSplit, FUN=ClonalitySamplePrint)
	
	clonalFreq = data.frame(data.table(clonalityFrame)[, list(Type=.N), by=c("Sample", "VDJCDR3")])
	clonalFreqCount = data.frame(data.table(clonalFreq)[, list(Count=.N), by=c("Sample", "Type")])
	clonalFreqCount$realCount = clonalFreqCount$Type * clonalFreqCount$Count
	clonalSum = data.frame(data.table(clonalFreqCount)[, list(Reads=sum(realCount)), by=c("Sample")])
	clonalFreqCount = merge(clonalFreqCount, clonalSum, by.x="Sample", by.y="Sample")