Mercurial > repos > davidvanzessen > report_clonality_igg

comparison RScript.r @ 1:81b9673b29be draft

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author davidvanzessen
date Tue, 28 Jan 2014 06:57:38 -0500
parents 08aa67564858
children 99834201251f
comparison
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0:08aa67564858 1:81b9673b29be
313 } 313 }
314 314
315 clonalityOverviewSplit = split(clonalityOverview, f=clonalityOverview$Sample) 315 clonalityOverviewSplit = split(clonalityOverview, f=clonalityOverview$Sample)
316 lapply(clonalityOverviewSplit, FUN=ClonalityOverviewPrint) 316 lapply(clonalityOverviewSplit, FUN=ClonalityOverviewPrint)
317 } 317 }
318
319 if("Functionality" %in% colnames(test))
320 {
321 newData = data.frame(data.table(PROD)[,list(unique=.N,
322 VH.DEL=mean(X3V.REGION.trimmed.nt.nb),
323 P1=mean(P3V.nt.nb),
324 N1=mean(N1.REGION.nt.nb),
325 P2=mean(P5D.nt.nb),
326 DEL.DH=mean(X5D.REGION.trimmed.nt.nb),
327 DH.DEL=mean(X3D.REGION.trimmed.nt.nb),
328 P3=mean(P3D.nt.nb),
329 N2=mean(N2.REGION.nt.nb),
330 P4=mean(P5J.nt.nb),
331 DEL.JH=mean(X5J.REGION.trimmed.nt.nb),
332 Total.Del=( mean(X3V.REGION.trimmed.nt.nb) +
333 mean(X5D.REGION.trimmed.nt.nb) +
334 mean(X3D.REGION.trimmed.nt.nb) +
335 mean(X5J.REGION.trimmed.nt.nb)),
336
337 Total.N=( mean(N1.REGION.nt.nb) +
338 mean(N2.REGION.nt.nb)),
339
340 Total.P=( mean(P3V.nt.nb) +
341 mean(P5D.nt.nb) +
342 mean(P3D.nt.nb) +
343 mean(P5J.nt.nb))),
344 by=c("Sample")])
345 write.table(newData, "junctionAnalysis.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F)
346 }