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charm (version 2.18.0)

readCharm: Read in McrBC/CHARM DNA methylation microarray data

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

Value

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

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).

References

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

See Also

methp, dmrFinder

Examples

Run this code
# See normalizeBetweenSamples

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