minfi (version 1.18.4)

mapToGenome-methods: 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

"mapToGenome"(object, mergeManifest = FALSE)
"mapToGenome"(object, mergeManifest = FALSE)
"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.

See Also

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