--- a/RScript.r	Tue Mar 11 09:21:57 2014 -0400
+++ b/RScript.r	Tue Mar 11 10:39:04 2014 -0400
@@ -243,14 +243,14 @@
 	}
 
     clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,c("Sample", "Replicate")])
-    lapply(clonalityFrameSplit, FUN=ClonalitySampleReplicatePrint)
+    #lapply(clonalityFrameSplit, FUN=ClonalitySampleReplicatePrint)
 
     ClonalitySamplePrint <- function(dat){
 	    write.table(dat, paste("clonality_", unique(dat$Sample) , ".tsv", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
 	}
 
     clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,"Sample"])
-    lapply(clonalityFrameSplit, FUN=ClonalitySamplePrint)
+    #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")])
@@ -315,3 +315,32 @@
 	clonalityOverviewSplit = split(clonalityOverview, f=clonalityOverview$Sample)
 	lapply(clonalityOverviewSplit, FUN=ClonalityOverviewPrint)
 }
+
+if("Functionality" %in% colnames(test))
+{
+	newData = data.frame(data.table(PROD)[,list(unique=.N, 
+				VH.DEL=mean(X3V.REGION.trimmed.nt.nb),
+				P1=mean(P3V.nt.nb),
+				N1=mean(N1.REGION.nt.nb),
+				P2=mean(P5D.nt.nb),
+				DEL.DH=mean(X5D.REGION.trimmed.nt.nb),
+				DH.DEL=mean(X3D.REGION.trimmed.nt.nb),
+				P3=mean(P3D.nt.nb),
+				N2=mean(N2.REGION.nt.nb),
+				P4=mean(P5J.nt.nb),
+				DEL.JH=mean(X5J.REGION.trimmed.nt.nb),
+				Total.Del=(	mean(X3V.REGION.trimmed.nt.nb) + 
+							mean(X5D.REGION.trimmed.nt.nb) + 
+							mean(X3D.REGION.trimmed.nt.nb) +
+							mean(X5J.REGION.trimmed.nt.nb)),
+							
+				Total.N=(	mean(N1.REGION.nt.nb) +
+							mean(N2.REGION.nt.nb)),
+							
+				Total.P=(	mean(P3V.nt.nb) +
+							mean(P5D.nt.nb) +
+							mean(P3D.nt.nb) +
+							mean(P5J.nt.nb))),
+				by=c("Sample")])
+	write.table(newData, "junctionAnalysis.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F)
+}