countGC: Count probe GC content

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

View source: R/charm.R

Description

Return the GC content for each probe

Usage

1
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.

Details

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

Value

a numeric vector

Author(s)

Martin Aryee <[email protected]>

See Also

readCharm

Examples

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	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)
	}

Bioconductor-mirror/charm documentation built on June 1, 2017, 5:29 a.m.