Mercurial > repos > davidvanzessen > report_clonality_tcell_igg
changeset 6:f4ff7450ef16 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Fri, 22 Aug 2014 11:02:20 -0400 |
| parents | fb219dfdcc15 |
| children | c7d3b68040d7 |
| files | RScript.r |
| diffstat | 1 files changed, 19 insertions(+), 5 deletions(-) [+] |
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--- a/RScript.r Thu Aug 21 10:44:40 2014 -0400 +++ b/RScript.r Fri Aug 22 11:02:20 2014 -0400 @@ -377,15 +377,15 @@ write.table(dat, paste("clonality_", unique(dat$Sample) , "_", unique(dat$Replicate), ".csv", sep=""), sep=",",quote=F,row.names=F,col.names=T) } - clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,c("Sample", "Replicate")]) - #lapply(clonalityFrameSplit, FUN=ClonalitySampleReplicatePrint) + clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,c("Sample", "Replicate")]) + #lapply(clonalityFrameSplit, FUN=ClonalitySampleReplicatePrint) - ClonalitySamplePrint <- function(dat){ + ClonalitySamplePrint <- function(dat){ write.table(dat, paste("clonality_", unique(dat$Sample) , ".csv", sep=""), sep=",",quote=F,row.names=F,col.names=T) } - clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,"Sample"]) - #lapply(clonalityFrameSplit, FUN=ClonalitySamplePrint) + clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,"Sample"]) + #lapply(clonalityFrameSplit, FUN=ClonalitySamplePrint) clonalFreq = data.frame(data.table(clonalityFrame)[, list(Type=.N), by=c("Sample", "VDJCDR3")]) clonalFreqCount = data.frame(data.table(clonalFreq)[, list(Count=.N), by=c("Sample", "Type")]) @@ -422,6 +422,20 @@ ReplicateSumSplit = split(ReplicateReads, f=ReplicateReads[,"Sample"]) lapply(ReplicateSumSplit, FUN=ReplicateSumPrint) + + writeClonalitySequences <- function(dat){ + for(i in c(2,3,4,5,6)){ + fltr = dat[dat$Type == i,] + if(length(fltr[,1]) == 0){ + next + } + tmp = clonalityFrame[clonalityFrame$Sample == fltr$Sample[1] & clonalityFrame$VDJCDR3 %in% fltr$VDJCDR3,] + tmp = tmp[order(tmp$VDJCDR3),] + write.table(tmp, paste("ClonalitySequences_", unique(dat[1])[1,1] , "_", i, ".csv", sep=""), sep=",",quote=F,na="-",row.names=F,col.names=T) + } + } + freqsplt = split(clonalFreq[clonalFreq$Type > 1,], clonalFreq[clonalFreq$Type > 1,]$Sample) + lapply(freqsplt, FUN=writeClonalitySequences) clonalFreqCountSum = data.frame(data.table(clonalFreqCount)[, list(Numerator=sum(WeightedCount, na.rm=T)), by=c("Sample")]) clonalFreqCount = merge(clonalFreqCount, clonalFreqCountSum, by.x="Sample", by.y="Sample", all.x=T)