mapToGenome-methods: Mapping methylation data to the genome

In hansenlab/minfi: Analyze Illumina Infinium DNA methylation arrays

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 [e-mail]

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)
}

hansenlab/minfi documentation built on Feb. 2, 2024, 11:23 a.m.