readCharm {charm} | R Documentation |
Read in DNA methylation microarray data from the McrBC/CHARM platform
readCharm(files, path = ".", ut = "_532.xys", md = "_635.xys", sampleKey, sampleNames = NULL, pkgname, type = NULL, ...)
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 |
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).
A TilingFeatureSet object. If the ff package is loaded before using this function, the output will contain ff rather than matrix objects.
Martin Aryee <aryee@jhu.edu>
www.biostat.jhsph.edu/~maryee/charm
# See normalizeBetweenSamples