| Previous changeset 36:edf2d5882b77 (2017-03-28) Next changeset 38:b6936fb52ab9 (2017-04-19) |
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modified:
report_clonality/RScript.r |
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| diff -r edf2d5882b77 -r f37e072affc0 report_clonality/RScript.r --- a/report_clonality/RScript.r Tue Mar 28 08:57:05 2017 -0400 +++ b/report_clonality/RScript.r Wed Apr 19 08:05:01 2017 -0400 |
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| @@ -977,7 +977,13 @@ #generate the "Sequences that are present in more than one replicate" dataset clonaltype.in.replicates = inputdata +clonaltype.in.replicates = na.omit(clonaltype.in.replicates) clonaltype = unlist(strsplit(clonaltype, ",")) + +clonaltype.in.replicates$clonaltype = do.call(paste, c(clonaltype.in.replicates[c(clonaltype, "Replicate")], sep = ":")) + +clonaltype.in.replicates = clonaltype.in.replicates[!duplicated(clonaltype.in.replicates$clonaltype),] + clonaltype = clonaltype[-which(clonaltype == "Sample")] clonaltype.in.replicates$clonaltype = do.call(paste, c(clonaltype.in.replicates[clonaltype], sep = ":")) @@ -990,7 +996,8 @@ clonaltype.in.replicates = clonaltype.in.replicates[clonaltype.in.replicates$clonaltype %in% clonaltype.counts$clonaltype,] clonaltype.in.replicates = merge(clonaltype.in.replicates, clonaltype.counts, by="clonaltype") -clonaltype.in.replicates = clonaltype.in.replicates[order(clonaltype.in.replicates$clonaltype),c("coincidence","clonaltype", "Sample", "Replicate", "ID", "Sequence")] +clonaltype.in.replicates = clonaltype.in.replicates[order(-clonaltype.in.replicates$coincidence, clonaltype.in.replicates$clonaltype, clonaltype.in.replicates$Replicate),c("coincidence","clonaltype", "Sample", "Replicate", "ID", "Sequence")] + write.table(clonaltype.in.replicates, "clonaltypes_replicates.txt" , sep="\t",quote=F,na="-",row.names=F,col.names=T) |