# HG changeset patch
# User davidvanzessen
# Date 1454063998 18000
# Node ID 379856bef228b3130134a7ddb86940bc8f8e8901
# Parent  371c568408e9410afe87c92714ea5a98253dc569
Uploaded

diff -r 371c568408e9 -r 379856bef228 report_clonality/RScript.r
--- a/report_clonality/RScript.r	Fri Jan 29 05:29:52 2016 -0500
+++ b/report_clonality/RScript.r	Fri Jan 29 05:39:58 2016 -0500
@@ -457,9 +457,10 @@
   completeVD = merge(completeVD, revVchain, by.x="Top.V.Gene", by.y="v.name", all.x=TRUE)
   completeVD = merge(completeVD, Dchain, by.x="Top.D.Gene", by.y="v.name", all.x=TRUE)
   
-  if(any(fltr, na.rm=T)){
-    completeVD[fltr,"relLength"] = 1
-  } 
+  fltr = is.nan(completeVD$relLength)
+  if(any(fltr)){
+	  completeVD[fltr,"relLength"] = 1
+  }
   
   VDList = split(completeVD, f=completeVD[,"Sample"])
   lapply(VDList, FUN=plotVD)
@@ -500,8 +501,8 @@
 completeVJ = merge(completeVJ, Jchain, by.x="Top.J.Gene", by.y="v.name", all.x=TRUE)
 
 fltr = is.nan(completeVJ$relLength)
-if(any(fltr, na.rm=T)){
-  completeVJ[fltr,"relLength"] = 1
+if(any(fltr)){
+	completeVJ[fltr,"relLength"] = 1
 }
 
 VJList = split(completeVJ, f=completeVJ[,"Sample"])
@@ -544,8 +545,8 @@
   completeDJ = merge(completeDJ, Jchain, by.x="Top.J.Gene", by.y="v.name", all.x=TRUE)
   
   fltr = is.nan(completeDJ$relLength)
-  if(any(fltr, na.rm=T)){
-    completeDJ[fltr,"relLength"] = 1
+  if(any(fltr)){
+	  completeDJ[fltr, "relLength"] = 1
   }
   
   DJList = split(completeDJ, f=completeDJ[,"Sample"])