# HG changeset patch
# User davidvanzessen
# Date 1499346472 14400
# Node ID a70dbcfa5d8a97cab0b214138219219d903b6b34
# Parent  106275b54470a5250d4d9758e0dd0f214e6a3f58
Uploaded

diff -r 106275b54470 -r a70dbcfa5d8a report_clonality/RScript.r
--- a/report_clonality/RScript.r	Tue May 30 07:26:33 2017 -0400
+++ b/report_clonality/RScript.r	Thu Jul 06 09:07:52 2017 -0400
@@ -990,7 +990,7 @@
 #generate the "Sequences that are present in more than one replicate" dataset
 clonaltype.in.replicates = inputdata
 clonaltype.in.replicates = clonaltype.in.replicates[clonaltype.in.replicates$Functionality %in% c("productive (see comment)","productive"),]
-clonaltype.in.replicates = na.omit(clonaltype.in.replicates)
+clonaltype.in.replicates = clonaltype.in.replicates[!(is.na(clonaltype.in.replicates$ID) | is.na(clonaltype.in.replicates$Top.V.Gene) | is.na(clonaltype.in.replicates$Top.J.Gene)),]
 clonaltype = unlist(strsplit(clonaltype, ","))
 
 clonaltype.in.replicates$clonaltype = do.call(paste, c(clonaltype.in.replicates[c(clonaltype, "Replicate")], sep = ":"))
@@ -1002,7 +1002,13 @@
 clonaltype.in.replicates$clonaltype = do.call(paste, c(clonaltype.in.replicates[clonaltype], sep = ":"))
 clonaltype.in.replicates = clonaltype.in.replicates[,c("clonaltype","Replicate", "ID", "Sequence", "Sample")]
 
+
+write.table(clonaltype.in.replicates, "clonaltypes_replicates_before_table.txt" , sep="\t",quote=F,na="-",row.names=F,col.names=T)
+
 clonaltype.counts = data.frame(table(clonaltype.in.replicates$clonaltype))
+
+write.table(clonaltype.counts, "clonaltypes_counts.txt" , sep="\t",quote=F,na="-",row.names=F,col.names=T)
+
 names(clonaltype.counts) = c("clonaltype", "coincidence")
 
 clonaltype.counts = clonaltype.counts[clonaltype.counts$coincidence > 1,]