From ae88630d521901bbd98f104a588e8a4115cb9bd1 Mon Sep 17 00:00:00 2001 From: corin Date: Fri, 18 Jun 2010 21:36:29 +0000 Subject: [PATCH] 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 --- R/tearsheet.r | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/R/tearsheet.r b/R/tearsheet.r index cfef0d45d..47bbe093c 100755 --- a/R/tearsheet.r +++ b/R/tearsheet.r @@ -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)