Mercurial > repos > davidvanzessen > mutation_analysis
changeset 9:4c4149fa0bcb draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 26 Mar 2015 08:53:41 -0400 |
| parents | 3f4b4ef46c7f |
| children | 4b83265b2686 |
| files | merge_and_filter.r |
| diffstat | 1 files changed, 6 insertions(+), 3 deletions(-) [+] |
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--- a/merge_and_filter.r Tue Mar 17 09:44:25 2015 -0400 +++ b/merge_and_filter.r Thu Mar 26 08:53:41 2015 -0400 @@ -15,8 +15,9 @@ summ = summ[summ$Functionality != "No results",] -tmp = summ[summ$chunk_hit_percentage >= 70 & summ$nt_hit_percentage >= 70,] -unmatched = summ[summ$chunk_hit_percentage < 70 & summ$nt_hit_percentage < 70,] +higher_than=(summ$chunk_hit_percentage >= 70 & summ$nt_hit_percentage >= 70) +tmp = summ[higher_than,] +unmatched = summ[!higher_than,] unmatched = unmatched[,c("Sequence.ID", "chunk_hit_percentage", "nt_hit_percentage", "start_locations", "best_match")] summ = tmp rm(tmp) @@ -29,7 +30,6 @@ result = merge(result, mutationstats[,!(names(mutationstats) %in% names(result)[-1])], by="Sequence.ID") result = merge(result, hotspots[,!(names(hotspots) %in% names(result)[-1])], by="Sequence.ID") - cleanup_columns = c("FR1.IMGT.Nb.of.mutations", "CDR1.IMGT.Nb.of.mutations", "FR2.IMGT.Nb.of.mutations", @@ -54,5 +54,8 @@ result = result[,!(names(result) %in% c("past"))] +print(paste("Number of rows in result:", nrow(result))) +print(paste("Number of rows in unmatched:", nrow(unmatched))) + write.table(x=result, file=output, sep="\t",quote=F,row.names=F,col.names=T) write.table(x=unmatched, file=unmatchedfile, sep="\t",quote=F,row.names=F,col.names=T)