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 1.30.0 Index]