Mercurial > repos > davidvanzessen > mutation_analysis
comparison tmp/igat.r @ 110:ade5cf6fd2dc draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Tue, 02 Aug 2016 08:30:23 -0400 |
| parents | e4957ad476a2 |
| children |
comparison
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| 109:0096cd454380 | 110:ade5cf6fd2dc |
|---|---|
| 13 merged = merged[!grepl("unmatched", merged$best_match),] | 13 merged = merged[!grepl("unmatched", merged$best_match),] |
| 14 | 14 |
| 15 for(f in list.files(imgt.dir, pattern="*.txt$")){ | 15 for(f in list.files(imgt.dir, pattern="*.txt$")){ |
| 16 #print(paste("filtering", f)) | 16 #print(paste("filtering", f)) |
| 17 path = paste(imgt.dir, f, sep="") | 17 path = paste(imgt.dir, f, sep="") |
| 18 dat = read.table(path, header=T, sep="\t", fill=T, quote="", stringsAsFactors=F) | 18 dat = read.table(path, header=T, sep="\t", fill=T, quote="", stringsAsFactors=F, check.names=FALSE) |
| 19 | 19 |
| 20 dat = dat[dat$Sequence.ID %in% merged$Sequence.ID,] | 20 dat = dat[dat[,"Sequence ID"] %in% merged$Sequence.ID,] |
| 21 | 21 |
| 22 if(nrow(dat) > 0 & grepl("^8_", f)){ #change the FR1 columns to 0 in the "8_..." file | 22 if(nrow(dat) > 0 & grepl("^8_", f)){ #change the FR1 columns to 0 in the "8_..." file |
| 23 dat[,grepl("^FR1", names(dat))] = 0 | 23 dat[,grepl("^FR1", names(dat))] = 0 |
| 24 } | 24 } |
| 25 | 25 |