Mercurial > repos > davidvanzessen > mutation_analysis

comparison tmp/igat.r @ 97:6e8dfbe164c6 draft

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Uploaded
author davidvanzessen
date Wed, 15 Jun 2016 04:48:41 -0400
parents a66eb1c5374c
children 86206431cbb0
comparison
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96:925efcd00c58 97:6e8dfbe164c6
2 2
3 imgt.dir = args[1] 3 imgt.dir = args[1]
4 merged.file = args[2] 4 merged.file = args[2]
5 5
6 merged = read.table(merged.file, header=T, sep="\t", fill=T, stringsAsFactors=F) 6 merged = read.table(merged.file, header=T, sep="\t", fill=T, stringsAsFactors=F)
7
8 merged = merged[!grepl("unmatched", merged$best_match),]
7 9
8 for(f in list.files(imgt.dir, pattern="*.txt$")){ 10 for(f in list.files(imgt.dir, pattern="*.txt$")){
9 print(paste("filtering", f)) 11 print(paste("filtering", f))
10 path = paste(imgt.dir, f, sep="") 12 path = paste(imgt.dir, f, sep="")
11 dat = read.table(path, header=T, sep="\t", fill=T, quote="", stringsAsFactors=F) 13 dat = read.table(path, header=T, sep="\t", fill=T, quote="", stringsAsFactors=F)