Mercurial > repos > davidvanzessen > report_clonality_igg

comparison RScript.r @ 5:99834201251f draft

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author davidvanzessen
date Mon, 10 Mar 2014 11:06:17 -0400
parents 81b9673b29be
children 18ac92a69ef1
comparison
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4:8803239b1770 5:99834201251f
241 ClonalitySampleReplicatePrint <- function(dat){ 241 ClonalitySampleReplicatePrint <- function(dat){
242 write.table(dat, paste("clonality_", unique(dat$Sample) , "_", unique(dat$Replicate), ".tsv", sep=""), sep="\t",quote=F,row.names=F,col.names=T) 242 write.table(dat, paste("clonality_", unique(dat$Sample) , "_", unique(dat$Replicate), ".tsv", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
243 } 243 }
244 244
245 clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,c("Sample", "Replicate")]) 245 clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,c("Sample", "Replicate")])
246 lapply(clonalityFrameSplit, FUN=ClonalitySampleReplicatePrint) 246 #lapply(clonalityFrameSplit, FUN=ClonalitySampleReplicatePrint)
247 247
248 ClonalitySamplePrint <- function(dat){ 248 ClonalitySamplePrint <- function(dat){
249 write.table(dat, paste("clonality_", unique(dat$Sample) , ".tsv", sep=""), sep="\t",quote=F,row.names=F,col.names=T) 249 write.table(dat, paste("clonality_", unique(dat$Sample) , ".tsv", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
250 } 250 }
251 251
252 clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,"Sample"]) 252 clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,"Sample"])
253 lapply(clonalityFrameSplit, FUN=ClonalitySamplePrint) 253 #lapply(clonalityFrameSplit, FUN=ClonalitySamplePrint)
254 254
255 clonalFreq = data.frame(data.table(clonalityFrame)[, list(Type=.N), by=c("Sample", "VDJCDR3")]) 255 clonalFreq = data.frame(data.table(clonalityFrame)[, list(Type=.N), by=c("Sample", "VDJCDR3")])
256 clonalFreqCount = data.frame(data.table(clonalFreq)[, list(Count=.N), by=c("Sample", "Type")]) 256 clonalFreqCount = data.frame(data.table(clonalFreq)[, list(Count=.N), by=c("Sample", "Type")])
257 clonalFreqCount$realCount = clonalFreqCount$Type * clonalFreqCount$Count 257 clonalFreqCount$realCount = clonalFreqCount$Type * clonalFreqCount$Count
258 clonalSum = data.frame(data.table(clonalFreqCount)[, list(Reads=sum(realCount)), by=c("Sample")]) 258 clonalSum = data.frame(data.table(clonalFreqCount)[, list(Reads=sum(realCount)), by=c("Sample")])
317 } 317 }
318 318
319 if("Functionality" %in% colnames(test)) 319 if("Functionality" %in% colnames(test))
320 { 320 {
321 newData = data.frame(data.table(PROD)[,list(unique=.N, 321 newData = data.frame(data.table(PROD)[,list(unique=.N,
322 VH.DEL=mean(X3V.REGION.trimmed.nt.nb), 322 VH.DEL=mean(X3V.REGION.trimmed.nt.nb),
323 P1=mean(P3V.nt.nb), 323 P1=mean(P3V.nt.nb),
324 N1=mean(N1.REGION.nt.nb), 324 N1=mean(N1.REGION.nt.nb),
325 P2=mean(P5D.nt.nb), 325 P2=mean(P5D.nt.nb),
326 DEL.DH=mean(X5D.REGION.trimmed.nt.nb), 326 DEL.DH=mean(X5D.REGION.trimmed.nt.nb),
327 DH.DEL=mean(X3D.REGION.trimmed.nt.nb), 327 DH.DEL=mean(X3D.REGION.trimmed.nt.nb),
328 P3=mean(P3D.nt.nb), 328 P3=mean(P3D.nt.nb),
329 N2=mean(N2.REGION.nt.nb), 329 N2=mean(N2.REGION.nt.nb),
330 P4=mean(P5J.nt.nb), 330 P4=mean(P5J.nt.nb),
331 DEL.JH=mean(X5J.REGION.trimmed.nt.nb), 331 DEL.JH=mean(X5J.REGION.trimmed.nt.nb),
332 Total.Del=( mean(X3V.REGION.trimmed.nt.nb) + 332 Total.Del=( mean(X3V.REGION.trimmed.nt.nb) +
333 mean(X5D.REGION.trimmed.nt.nb) + 333 mean(X5D.REGION.trimmed.nt.nb) +
334 mean(X3D.REGION.trimmed.nt.nb) + 334 mean(X3D.REGION.trimmed.nt.nb) +
335 mean(X5J.REGION.trimmed.nt.nb)), 335 mean(X5J.REGION.trimmed.nt.nb)),
336 336
337 Total.N=( mean(N1.REGION.nt.nb) + 337 Total.N=( mean(N1.REGION.nt.nb) +
338 mean(N2.REGION.nt.nb)), 338 mean(N2.REGION.nt.nb)),
339 339
340 Total.P=( mean(P3V.nt.nb) + 340 Total.P=( mean(P3V.nt.nb) +
341 mean(P5D.nt.nb) + 341 mean(P5D.nt.nb) +
342 mean(P3D.nt.nb) + 342 mean(P3D.nt.nb) +
343 mean(P5J.nt.nb))), 343 mean(P5J.nt.nb))),
344 by=c("Sample")]) 344 by=c("Sample")])
345 write.table(newData, "junctionAnalysis.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F) 345 write.table(newData, "junctionAnalysis.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F)
346 } 346 }