zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Support for command-line arguments. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6055 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
droazen 2011-06-22 22:55:05 +00:00
parent d9973d3da7
commit 3392c67e0f
1 changed files with 10 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

12
R/exomePreQC.R
View File

@ -1,6 +1,14 @@
require('ggplot2')
data <- read.table('GoT2D_exomes_batch_005.tsv',header=T)
args = commandArgs(TRUE)
onCMDLine = ! is.na(args[1])
if ( onCMDLine ) {
inputTSV = args[1]
outputPDF = args[2]
}
data <- read.table(inputTSV,header=T)
fingerprint_lods = list()
for(i in 1:nrow(data)) {
@ -9,7 +17,7 @@ for(i in 1:nrow(data)) {
fingerprint_lod_order = order(unlist(lapply(fingerprint_lods,median),use.names=F))
pdf('T2D.pdf')
pdf(outputPDF)
boxplot(fingerprint_lods[fingerprint_lod_order],las=3,main='Fingerprint LOD Scores By Sample',xlab='Sample',ylab='LOD Score Distribution',cex.axis=0.65)
qplot(sample,GENOME_SIZE,data=data) + opts(title='Genome Size per Sample')
qplot(sample,PCT_SELECTED_BASES,data=data) + opts(title='On+Near Bait Bases/PF Bases Aligned per Sample')