Mercurial > repos > davidvanzessen > argalaxy_tools

diff report_clonality/RScript.r @ 19:672d5e010b1f draft

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Uploaded
author davidvanzessen
date Fri, 25 Dec 2015 05:35:06 -0500
parents 431797cd74c8
children f2010de70741
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line diff
--- a/report_clonality/RScript.r	Mon Dec 21 07:23:37 2015 -0500
+++ b/report_clonality/RScript.r	Fri Dec 25 05:35:06 2015 -0500
@@ -584,6 +584,14 @@
 if(all(imgtcolumns %in% colnames(inputdata)))
 {
   print("found IMGT columns, running junction analysis")
+  
+  if(locus %in% c("IGK","IGL", "TRA", "TRG")){
+	  print("VJ recombination, using N column for junction analysis")
+	  print(names(PRODF))
+	  print(head(PRODF$N.REGION.nt.nb, 30))
+	  PRODF$N1.REGION.nt.nb = PRODF$N.REGION.nt.nb
+  }
+  
   newData = data.frame(data.table(PRODF)[,list(unique=.N, 
                                                VH.DEL=mean(.SD$X3V.REGION.trimmed.nt.nb, na.rm=T),
                                                P1=mean(.SD$P3V.nt.nb, na.rm=T),