Mercurial > repos > davidvanzessen > shm_csr

comparison shm_csr.r @ 62:aa8d37bd1930 draft

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author davidvanzessen
date Tue, 05 Dec 2017 10:57:13 -0500
parents 77a7ac76c7b9
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61:275e759e7985 62:aa8d37bd1930
8 genes = unlist(strsplit(args[2], ",")) 8 genes = unlist(strsplit(args[2], ","))
9 outputdir = args[3] 9 outputdir = args[3]
10 empty.region.filter = args[4] 10 empty.region.filter = args[4]
11 setwd(outputdir) 11 setwd(outputdir)
12 12
13 dat = read.table(input, header=T, sep="\t", fill=T, stringsAsFactors=F) 13 #dat = read.table(input, header=T, sep="\t", fill=T, stringsAsFactors=F)
14
15 dat = data.frame(fread(input, sep="\t", header=T, stringsAsFactors=F)) #fread because read.table suddenly skips certain rows...
14 16
15 if(length(dat$Sequence.ID) == 0){ 17 if(length(dat$Sequence.ID) == 0){
16 setwd(outputdir) 18 setwd(outputdir)
17 result = data.frame(x = rep(0, 5), y = rep(0, 5), z = rep(NA, 5)) 19 result = data.frame(x = rep(0, 5), y = rep(0, 5), z = rep(NA, 5))
18 row.names(result) = c("Number of Mutations (%)", "Transition (%)", "Transversions (%)", "Transitions at G C (%)", "Targeting of G C (%)") 20 row.names(result) = c("Number of Mutations (%)", "Transition (%)", "Transversions (%)", "Transitions at G C (%)", "Targeting of G C (%)")