charm (version 2.18.0)

countGC: Count probe GC content

Description

Return the GC content for each probe

Usage

countGC(dat, type = "pm", idx)

Arguments

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.

Value

a numeric vector

Details

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

See Also

readCharm

Examples

	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)
	}