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modified:
merge_and_filter.r shm_csr.xml |
| b |
| diff -r 1ad34508be98 -r 3b5fe323f563 merge_and_filter.r --- a/merge_and_filter.r Tue Jul 18 05:03:55 2017 -0400 +++ b/merge_and_filter.r Wed Jul 26 10:24:49 2017 -0400 |
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| @@ -219,7 +219,9 @@ if(filter.unique != "no"){ clmns = names(result) - if(empty.region.filter == "leader"){ + if(filter.unique == "remove_vjaa"){ + result$unique.def = paste(result$V.GENE.and.allele, result$J.GENE.and.allele, result$CDR3.IMGT.seq) + } 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$CDR3.IMGT.seq) } else if(empty.region.filter == "FR1"){ result$unique.def = paste(result$CDR1.IMGT.seq, result$FR2.IMGT.seq, result$CDR2.IMGT.seq, result$FR3.IMGT.seq, result$CDR3.IMGT.seq) @@ -229,7 +231,7 @@ result$unique.def = paste(result$CDR2.IMGT.seq, result$FR3.IMGT.seq, result$CDR3.IMGT.seq) } - if(filter.unique == "remove"){ + if(grepl("remove", filter.unique)){ result = result[duplicated(result$unique.def) | duplicated(result$unique.def, fromLast=T),] unique.defs = data.frame(table(result$unique.def)) unique.defs = unique.defs[unique.defs$Freq >= filter.unique.count,] |
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| diff -r 1ad34508be98 -r 3b5fe323f563 shm_csr.xml --- a/shm_csr.xml Tue Jul 18 05:03:55 2017 -0400 +++ b/shm_csr.xml Wed Jul 26 10:24:49 2017 -0400 |
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| @@ -33,6 +33,7 @@ <conditional name="filter_unique"> <param name="filter_unique_select" type="select" label="Filter unique sequences" help="See below for an example."> <option value="remove" selected="true">Remove uniques (Based on nucleotide sequence + C)</option> + <option value="remove_vjaa">Remove uniques (Based on V+J+CDR3 (AA))</option> <option value="keep">Keep uniques (Based on nucleotide sequence + C)</option> <option value="no">No</option> </param> |