diff RScript.r @ 1:81b9673b29be draft

Uploaded

--- a/RScript.r	Tue Jan 28 03:44:44 2014 -0500
+++ b/RScript.r	Tue Jan 28 06:57:38 2014 -0500
@@ -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)
+}
\ No newline at end of file