Mercurial > repos > davidvanzessen > combined_immune_repertoire_pipeline
changeset 4:87fb14480352 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Fri, 22 Nov 2013 08:12:53 -0500 |
| parents | 2b1d3d6843e8 |
| children | ba2ef103d26e |
| files | RScript.r |
| diffstat | 1 files changed, 3 insertions(+), 1 deletions(-) [+] |
line wrap: on
line diff
--- a/RScript.r Fri Nov 22 08:12:46 2013 -0500 +++ b/RScript.r Fri Nov 22 08:12:53 2013 -0500 @@ -5,6 +5,7 @@ inFile = args[1] outFile = args[2] outDir = args[3] +clonalType = args[4] if (!("gridExtra" %in% rownames(installed.packages()))) { install.packages("gridExtra", repos="http://cran.xl-mirror.nl/") @@ -33,7 +34,8 @@ test$Top.D.Gene = gsub("[*]([0-9]+)", "", test$Top.D.Gene) test$Top.J.Gene = gsub("[*]([0-9]+)", "", test$Top.J.Gene) -test$VDJCDR3 = do.call(paste, c(test[c("Top.V.Gene", "Top.D.Gene", "Top.J.Gene","CDR3.Seq.DNA")], sep = ":")) +#test$VDJCDR3 = do.call(paste, c(test[c("Top.V.Gene", "Top.D.Gene", "Top.J.Gene","CDR3.Seq.DNA")], sep = ":")) +test$VDJCDR3 = do.call(paste, c(test[unlist(strsplit(clonalType, ","))], sep = ":")) PROD = test[test$VDJ.Frame != "In-frame with stop codon" & test$VDJ.Frame != "Out-of-frame" & test$CDR3.Found.How != "NOT_FOUND" , ]