initial check-in

SVN: 21247

deep_sequencing_unit/source/R/numberOfOccurrences.R

+# 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()
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