mapToGenome-methods {minfi} | R Documentation |
Mapping Ilumina methylation array data to the genome using an annotation package. Depending on the genome, not all methylation loci may have a genomic position.
## S4 method for signature 'MethylSet' mapToGenome(object, mergeManifest = FALSE) ## S4 method for signature 'MethylSet' mapToGenome(object, mergeManifest = FALSE) ## S4 method for signature 'RGChannelSet' mapToGenome(object, ...)
object |
Either a |
mergeManifest |
Should the information in the associated manifest
package be merged into the location |
... |
Passed to the method for |
FIXME: details on the MethylSet method.
The RGChannelSet
method of this function is a convenience
function: the RGChannelSet
is first transformed into a
MethylSet
using preprocessRaw
. The resulting
MethylSet
is then mapped directly to the genome.
This function silently drops loci which cannot be mapped to a genomic position, based on the associated annotation package.
An object of class GenomicMethylSet
or GenomicRatioSet
.
Kasper Daniel Hansen khansen@jhsph.edu
GenomicMethylSet
for the output object and
MethylSet
for the input object. Also,
getLocations
obtains the genomic locations for a given object.
if (require(minfiData)) { ## MsetEx.sub is a small subset of MsetEx; ## only used for computational speed. GMsetEx.sub <- mapToGenome(MsetEx.sub) }