Mercurial > repos > davidvanzessen > combined_immune_repertoire_pipeline

comparison RScript.r @ 15:c69d9262c66d draft

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author davidvanzessen
date Tue, 14 Jan 2014 04:33:44 -0500
parents b07346fe54b4
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14:b07346fe54b4 15:c69d9262c66d
265 clonalFreqCount = merge(clonalFreqCount, CT, by.x="Type", by.y="Type", all.x=T) 265 clonalFreqCount = merge(clonalFreqCount, CT, by.x="Type", by.y="Type", all.x=T)
266 clonalFreqCount$WeightedCount = clonalFreqCount$Count * clonalFreqCount$Weight 266 clonalFreqCount$WeightedCount = clonalFreqCount$Count * clonalFreqCount$Weight
267 267
268 ReplicateReads = data.frame(data.table(clonalityFrame)[, list(Type=.N), by=c("Sample", "Replicate", "VDJCDR3")]) 268 ReplicateReads = data.frame(data.table(clonalityFrame)[, list(Type=.N), by=c("Sample", "Replicate", "VDJCDR3")])
269 ReplicateReads = data.frame(data.table(ReplicateReads)[, list(Reads=.N), by=c("Sample", "Replicate")]) 269 ReplicateReads = data.frame(data.table(ReplicateReads)[, list(Reads=.N), by=c("Sample", "Replicate")])
270 clonalFreqCount$Reads = as.numeric(clonalFreqCount$Reads)
270 ReplicateReads$squared = ReplicateReads$Reads * ReplicateReads$Reads 271 ReplicateReads$squared = ReplicateReads$Reads * ReplicateReads$Reads
271 272
272 ReplicatePrint <- function(dat){ 273 ReplicatePrint <- function(dat){
273 write.table(dat[-1], paste("ReplicateReads_", unique(dat[1])[1,1] , ".csv", sep=""), sep=",",quote=F,na="-",row.names=F,col.names=F) 274 write.table(dat[-1], paste("ReplicateReads_", unique(dat[1])[1,1] , ".csv", sep=""), sep=",",quote=F,na="-",row.names=F,col.names=F)
274 } 275 }