Mercurial > repos > davidvanzessen > combined_immune_repertoire_imgt

comparison RScript.r @ 8:141b0362603e draft

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author davidvanzessen
date Fri, 10 Jan 2014 03:42:43 -0500
parents c134f2d0a484
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comparison
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7:c134f2d0a484 8:141b0362603e
287 ReplicateSumSplit = split(ReplicateReads, f=ReplicateReads[,"Sample"]) 287 ReplicateSumSplit = split(ReplicateReads, f=ReplicateReads[,"Sample"])
288 lapply(ReplicateSumSplit, FUN=ReplicateSumPrint) 288 lapply(ReplicateSumSplit, FUN=ReplicateSumPrint)
289 289
290 clonalFreqCountSum = data.frame(data.table(clonalFreqCount)[, list(Numerator=sum(WeightedCount, na.rm=T)), by=c("Sample")]) 290 clonalFreqCountSum = data.frame(data.table(clonalFreqCount)[, list(Numerator=sum(WeightedCount, na.rm=T)), by=c("Sample")])
291 clonalFreqCount = merge(clonalFreqCount, clonalFreqCountSum, by.x="Sample", by.y="Sample", all.x=T) 291 clonalFreqCount = merge(clonalFreqCount, clonalFreqCountSum, by.x="Sample", by.y="Sample", all.x=T)
292 292 clonalFreqCount$ReadsSum = as.numeric(clonalFreqCount$ReadsSum) #prevent integer overflow
293 clonalFreqCount$Denominator = (((clonalFreqCount$ReadsSum * clonalFreqCount$ReadsSum) - clonalFreqCount$ReadsSquaredSum) / 2) 293 clonalFreqCount$Denominator = (((clonalFreqCount$ReadsSum * clonalFreqCount$ReadsSum) - clonalFreqCount$ReadsSquaredSum) / 2)
294 clonalFreqCount$Result = (clonalFreqCount$Numerator + 1) / (clonalFreqCount$Denominator + 1) 294 clonalFreqCount$Result = (clonalFreqCount$Numerator + 1) / (clonalFreqCount$Denominator + 1)
295 295
296 ClonalityScorePrint <- function(dat){ 296 ClonalityScorePrint <- function(dat){
297 write.table(dat$Result, paste("ClonalityScore_", unique(dat[1])[1,1] , ".csv", sep=""), sep=",",quote=F,na="-",row.names=F,col.names=F) 297 write.table(dat$Result, paste("ClonalityScore_", unique(dat[1])[1,1] , ".csv", sep=""), sep=",",quote=F,na="-",row.names=F,col.names=F)