Mercurial > repos > davidvanzessen > combined_immune_repertoire_imgt
changeset 3:e1aa99d86a8a draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Mon, 09 Dec 2013 07:13:51 -0500 |
| parents | 1c5927d0a4ce |
| children | 8ba0fd5b03a1 |
| files | RScript.r |
| diffstat | 1 files changed, 17 insertions(+), 0 deletions(-) [+] |
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--- a/RScript.r Mon Dec 09 06:09:37 2013 -0500 +++ b/RScript.r Mon Dec 09 07:13:51 2013 -0500 @@ -231,6 +231,23 @@ 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