From c1af38fd4afbfd097e2bb10939689677e93440dc Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Wed, 11 May 2011 15:20:57 +0000
Subject: [PATCH] initial check-in

SVN: 21247
---
 .../source/R/numberOfOccurrences.R            | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 deep_sequencing_unit/source/R/numberOfOccurrences.R

diff --git a/deep_sequencing_unit/source/R/numberOfOccurrences.R b/deep_sequencing_unit/source/R/numberOfOccurrences.R
new file mode 100644
index 00000000000..4183dd9eb2b
--- /dev/null
+++ b/deep_sequencing_unit/source/R/numberOfOccurrences.R
@@ -0,0 +1,19 @@
+# Taken from http://www.bioconductor.org/help/workflows/high-throughput-sequencing/
+
+## Load packages; also loads Biostrings, IRanges, ...
+library(multicore)
+library(ShortRead)
+
+args <- commandArgs(TRUE)
+seq <- readFastq(args[1])
+
+pdf(file=paste(args[1],"NumberOfOccurrences.pdf", sep="_"))
+
+## Calculate and plot cumulative reads vs. occurrences
+tbl <- tables(seq)[[2]]
+xyplot(cumsum(nReads * nOccurrences) ~ nOccurrences, tbl, 
+scales=list(x=list(log=TRUE)), main=args[1], type="b", pch=20,
+xlab="Number of Occurrences", 
+ylab="Cumulative Number of Reads")
+
+dev.off()
\ No newline at end of file
-- 
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