From 237f73c1b1a6e842a2df6b16c83e26ec46300325 Mon Sep 17 00:00:00 2001 From: droazen Date: Wed, 22 Jun 2011 22:54:59 +0000 Subject: [PATCH] Initial fingerprint boxplot for exome PreQC metrics. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6053 348d0f76-0448-11de-a6fe-93d51630548a --- R/exomePreQC.R | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 R/exomePreQC.R diff --git a/R/exomePreQC.R b/R/exomePreQC.R new file mode 100644 index 000000000..536020d2b --- /dev/null +++ b/R/exomePreQC.R @@ -0,0 +1,10 @@ +data <- read.table('GoT2D_exomes_batch_005.tsv',header=T) + +fingerprint_lods = list() +for(i in 1:nrow(data)) { + fingerprint_lods[[as.character(data$sample[i])]] <- eval(parse(text=data$FINGERPRINT_LODS[i])) +} + +fingerprint_lod_order = order(unlist(lapply(fingerprint_lods,median),use.names=F)) + +boxplot(fingerprint_lods[fingerprint_lod_order],las=3,main='Fingerprint LOD Scores By Sample',xlab='Sample',ylab='LOD Score Distribution',cex.axis=0.65)