readCharm: Read in McrBC/CHARM DNA methylation microarray data

In charm: Analysis of DNA methylation data from CHARM microarrays

Description

Read in DNA methylation microarray data from the McrBC/CHARM platform

Usage

readCharm(files, path = ".", ut = "_532.xys", md = "_635.xys", 
	sampleKey, sampleNames = NULL, pkgname, type = NULL, ...)

Arguments

files	a vector of xys filenames
path	the path to the xys files
ut	the file ending that designates untreated channel files
md	the file ending that designates methyl-depleted channel files
sampleKey	a data frame with sample description information. One line per xys file.
sampleNames	a vector of names to use for the samples. One line per xys file.
pkgname	the annotation package name
type	deprecated option
...	additional options passed on to read.xysfiles2

Details

This function is a convenience wrapper to read.xysfiles2 to simplify reading in DNA methylation data from the Nimblegen McrBC/CHARM microarray platform. It makes guesses about the extensions used for the methyl-depleted (md) and untreated channels (ut).

Value

A TilingFeatureSet object. If the ff package is loaded before using this function, the output will contain ff rather than matrix objects.

Author(s)

Martin Aryee <[e-mail]>

References

www.biostat.jhsph.edu/~maryee/charm

See Also

methp, dmrFinder

Examples

# See normalizeBetweenSamples

charm documentation built on May 6, 2019, 2:29 a.m.