Mercurial > repos > davidvanzessen > argalaxy_tools
changeset 37:f37e072affc0 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Wed, 19 Apr 2017 08:05:01 -0400 |
| parents | edf2d5882b77 |
| children | b6936fb52ab9 |
| files | report_clonality/RScript.r |
| diffstat | 1 files changed, 8 insertions(+), 1 deletions(-) [+] |
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--- 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 @@ -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)