Mercurial > repos > davidvanzessen > shm_csr
diff merge_and_filter.r @ 96:385dea3c6cb5 draft
planemo upload commit 423a48569c69301fdbf893ac3a649128404dfff5
| author | rhpvorderman |
|---|---|
| date | Fri, 05 Jan 2024 08:53:22 +0000 |
| parents | 8fcf31272f6e |
| children |
line wrap: on
line diff
--- a/merge_and_filter.r Mon Mar 27 13:11:53 2023 +0000 +++ b/merge_and_filter.r Fri Jan 05 08:53:22 2024 +0000 @@ -183,6 +183,7 @@ } else if(empty.region.filter == "FR2"){ result = result[result$CDR2.IMGT.seq != "" & result$FR3.IMGT.seq != "", ] } +# If empty region filter is None, nothing happens. print(paste("After removal sequences that are missing a gene region:", nrow(result))) filtering.steps = rbind(filtering.steps, c("After removal sequences that are missing a gene region", nrow(result))) @@ -219,7 +220,7 @@ clmns = names(result) if(filter.unique == "remove_vjaa"){ result$unique.def = paste(result$VGene, result$JGene, result$CDR3.IMGT.AA) - } else if(empty.region.filter == "leader"){ + } else if(empty.region.filter == "leader" || empty.region.filter == "None"){ 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$CDR3.IMGT.seq) } else if(empty.region.filter == "FR1"){ result$unique.def = paste(result$CDR1.IMGT.seq, result$FR2.IMGT.seq, result$CDR2.IMGT.seq, result$FR3.IMGT.seq, result$CDR3.IMGT.seq)