mapToGenome-methods: Mapping methylation data to the genome
In minfi: Analyze Illumina Infinium DNA methylation arrays

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

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 `MethylSet`, a `RGChannelSet` or a `RatioSet`.
`mergeManifest`	Should the information in the associated manifest package be merged into the location `GRanges`?
`...`	Passed to the method for `MethylSet`.

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)
}