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This script produces tearsheet and data processing report figures and tables when given Squid and Firehose produced data 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3594 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
corin 2010-06-18 21:36:29 +00:00
parent 1e06d2bf68
commit ae88630d52
1 changed files with 3 additions and 3 deletions
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6
R/tearsheet.r
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@ -1,5 +1,5 @@
#Before executing this file, save squid files as csv, then as tab deliminated files with only the column values as the header, change the format of all cells to numbers. Assign the path to these files to "samples" and "lanes" respectively.
#testcomment
args<-commandArgs(TRUE)
lanes<-args[1]
samples<-args[2]
@ -152,8 +152,8 @@ if(is.na(sample_sets)){
print(paste("Read Legnths: ", mean.mrl.samp, " +/- ", sd.mrl.samp, sep=""), quote = FALSE);
print(paste("Reads per lane: ", mean.read.lane, " +/- ", sd.read.lane, sep=""), quote = FALSE);
print(paste("Reads per sample: ", mean.read.samp, " +/- ", sd.read.samp, sep=""), quote = FALSE);
print(paste("Used bases per lane: ", mean.read.lane, " +/- ", sd.read.lane, sep=""), quote = FALSE);
print(paste("Used bases per sample: ", mean.read.samp, " +/- ", sd.read.samp, sep=""), quote = FALSE)
print(paste("Used bases per lane: ", mean.ub.lane, " +/- ", sd.ub.lane, sep=""), quote = FALSE);
print(paste("Used bases per sample: ", mean.ub.samp, " +/- ", sd.ub.samp, sep=""), quote = FALSE)
print(paste("Average target coverage per lane: ", mean.cov.lane, " +/- ", sd.cov.lane, sep=""), quote = FALSE);
print(paste("Average target coverage per sample: ", mean.cov.samp, " +/- ", sd.cov.samp, sep=""), quote = FALSE);
print(paste("% loci covered to 10x per lane: ", mean.10x.lane, "% +/- ", sd.10x.lane, "%", sep=""), quote = FALSE)