countGC: Count probe GC content
In charm: Analysis of DNA methylation data from CHARM microarrays

Description Usage Arguments Details Value Author(s) See Also Examples

Return the GC content for each probe

1	countGC(dat, type = "pm", idx)

`dat`	a TilingFeatureSet object
`type`	pm or bg probes
`idx`	An optional vector of probe indices for which to return GC content. If not specified, values for all pm (or bg) probes will be returned.

This function returns the sum of #G + #C in the pm or bg probes.

a numeric vector

Martin Aryee <aryee@jhu.edu>

readCharm

	if (require(charmData)) {
		phenodataDir <- system.file("extdata", package="charmData")
		pd <- read.delim(file.path(phenodataDir, "phenodata.txt"))
		pd <- subset(pd, sampleID=="441_liver")
		dataDir <- system.file("data", package="charmData")
		setwd(dataDir)
		rawData <- readCharm(files=pd$filename, sampleKey=pd)
		ngc <- countGC(rawData)
		head(ngc)
	}