# HG changeset patch
# User davidvanzessen
# Date 1386591231 18000
# Node ID e1aa99d86a8ac6708b62cbeec6b6d67b8c812cfc
# Parent  1c5927d0a4ce56fe903257c533fdc7faac6b03ac
Uploaded

diff -r 1c5927d0a4ce -r e1aa99d86a8a RScript.r
--- a/RScript.r	Mon Dec 09 06:09:37 2013 -0500
+++ b/RScript.r	Mon Dec 09 07:13:51 2013 -0500
@@ -231,6 +231,23 @@
 	clonalityFrame = PROD
 	clonalityFrame$ReplicateConcat = do.call(paste, c(clonalityFrame[c("VDJCDR3", "Sample", "Replicate")], sep = ":"))
 	clonalityFrame = clonalityFrame[!duplicated(clonalityFrame$ReplicateConcat), ]
+	
+	write.table(clonalityFrame, "clonalityComplete.tsv", sep="\t",quote=F,row.names=T,col.names=T)
+
+	ClonalitySampleReplicatePrint <- function(dat){
+	    write.table(dat, paste("clonality_", unique(dat$Sample) , "_", unique(dat$Replicate), ".tsv", sep=""), sep="\t",quote=F,row.names=T,col.names=T)
+	}
+
+    clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,c("Sample", "Replicate")])
+    lapply(clonalityFrameSplit, FUN=ClonalitySampleReplicatePrint)
+
+    ClonalitySamplePrint <- function(dat){
+	    write.table(dat, paste("clonality_", unique(dat$Sample) , ".tsv", sep=""), sep="\t",quote=F,row.names=T,col.names=T)
+	}
+
+    clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,"Sample"])
+    lapply(clonalityFrameSplit, FUN=ClonalitySamplePrint)
+	
 	clonalFreq = data.frame(data.table(clonalityFrame)[, list(Type=.N), by=c("Sample", "VDJCDR3")])
 	clonalFreqCount = data.frame(data.table(clonalFreq)[, list(Count=.N), by=c("Sample", "Type")])
 	clonalFreqCount$realCount = clonalFreqCount$Type * clonalFreqCount$Count