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Small whitespace changes

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1 parent b76e4a8 commit c8ac270ac2ed15c3918e1ff9f7a093ded62cb1d9 @SeeLittle committed Dec 15, 2011
Showing with 0 additions and 11 deletions.
  1. +0 −11 mariekeLN_BRCAness_pc.R
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11 mariekeLN_BRCAness_pc.R
@@ -10,8 +10,6 @@ setwd('D:/MariekeLN')
require(KCsmart)
data(hsMirrorLocs)
-
-
## unavg DNAcopy file of 135k profile
tmp135 <- read.table('ng135kprofile_unavgDNAcopy.txt',
sep="\t", header=T, stringsAsFactors=F)
@@ -24,8 +22,6 @@ clin <- read.table('Clin_data_tumorLN-131211.txt', sep="\t", header=T, stringsAs
# for plotting etc
clin$id <- paste(clin$NR, clin$Type, sep="")
-
-
# folder with DNAcopy files
setwd('DNACopy')
@@ -35,14 +31,10 @@ files <- dir(pattern='.txt' )
files <- cbind(files, short= gsub('(^[0-9NGA]{4,9}).*', '\\1', files))
# bind name of the sample
lookup <- cbind(files, clin$id[match(files[,'short'], clin$File_name)] )
-
-
-
# create folder for mapped profiles and for plots of the mapped profiles
dir.create('mapped')
dir.create('plots')
-
# loop over all txt files
for (i in 1:nrow(lookup)) {
# read 720k profile
@@ -85,8 +77,6 @@ for (i in 1:nrow(lookup)) {
}
-
-
# Perform classification of nimblegen profiles. For this I've loaded the mapped files into
# the classifier tool. There are 3 models currently which are exactly the same as the BRCA1
# 191 (published by Simon) and 371 (published by Marieke) classifers and the BRCA2 classifier.
@@ -167,7 +157,6 @@ rat135$chrom <- fixChrom(rat135$chrom)
seg135$chrom <- fixChrom(seg135$chrom)
dir.create('translationPlots')
-
for (i in 3:(ncol(rat135))) {
png(paste('translationPlots/', colnames(rat135)[i],'.png', sep=""), height=768, width=1024)

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