mapToGenome-methods {minfi}R Documentation

Mapping methylation data to the genome

Description

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.

Usage


## 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, ...)

Arguments

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.

Details

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.

Value

An object of class GenomicMethylSet or GenomicRatioSet.

Author(s)

Kasper Daniel Hansen khansen@jhsph.edu

See Also

GenomicMethylSet for the output object and MethylSet for the input object. Also, getLocations obtains the genomic locations for a given object.

Examples

if (require(minfiData)) {
  ## MsetEx.sub is a small subset of MsetEx;
  ## only used for computational speed.
  GMsetEx.sub <- mapToGenome(MsetEx.sub)
}

[Package minfi version 1.36.0 Index]