Mercurial > repos > davidvanzessen > shm_csr
changeset 61:275e759e7985 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Fri, 18 Aug 2017 10:43:31 -0400 |
| parents | 3b5fe323f563 |
| children | aa8d37bd1930 |
| files | merge_and_filter.r |
| diffstat | 1 files changed, 4 insertions(+), 2 deletions(-) [+] |
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--- a/merge_and_filter.r Wed Jul 26 10:24:49 2017 -0400 +++ b/merge_and_filter.r Fri Aug 18 10:43:31 2017 -0400 @@ -220,7 +220,7 @@ if(filter.unique != "no"){ clmns = names(result) if(filter.unique == "remove_vjaa"){ - result$unique.def = paste(result$V.GENE.and.allele, result$J.GENE.and.allele, result$CDR3.IMGT.seq) + result$unique.def = paste(result$VGene, result$JGene, result$CDR3.IMGT.AA) } else if(empty.region.filter == "leader"){ result$unique.def = paste(result$FR1.IMGT.seq, result$CDR1.IMGT.seq, result$FR2.IMGT.seq, result$CDR2.IMGT.seq, result$FR3.IMGT.seq, result$CDR3.IMGT.seq) } else if(empty.region.filter == "FR1"){ @@ -238,7 +238,9 @@ result = result[result$unique.def %in% unique.defs$Var1,] } - result$unique.def = paste(result$unique.def, gsub(",.*", "", result$best_match)) #keep the unique sequences that are in multiple classes, gsub so the unmatched don't have a class after it + if(filter.unique != "remove_vjaa"){ + result$unique.def = paste(result$unique.def, gsub(",.*", "", result$best_match)) #keep the unique sequences that are in multiple classes, gsub so the unmatched don't have a class after it + } result = result[!duplicated(result$unique.def),] }