GenomicRatioSet-class {minfi} | R Documentation

## GenomicRatioSet instances

### Description

This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic location.

### Usage

    ## Constructor

    GenomicRatioSet(gr = GRanges(), Beta = NULL, M = NULL,
                    CN = NULL, annotation = "",
                    preprocessMethod = "", ...)

    ## Data extraction / Accessors

    ## S4 method for signature 'GenomicRatioSet'
    getBeta(object)
    ## S4 method for signature 'GenomicRatioSet'
    getM(object)
    ## S4 method for signature 'GenomicRatioSet'
    getCN(object)
    ## S4 method for signature 'GenomicRatioSet'
    pData(object)
    ## S4 method for signature 'GenomicRatioSet'
    sampleNames(object)
    ## S4 method for signature 'GenomicRatioSet'
    featureNames(object)
    ## S4 method for signature 'GenomicRatioSet'
    annotation(object)
    ## S4 method for signature 'GenomicRatioSet'
    preprocessMethod(object)
    ## S4 method for signature 'GenomicRatioSet'
    mapToGenome(object, ...)

### Arguments

`object` | A `GenomicRatioSet`.
`gr` | A `GRanges` object.
`Beta` | A matrix of beta values (optional, see details).
`M` | A matrix of M values (optional, see details).
`CN` | A matrix of copy number values.
`annotation` | An annotation character string.
`preprocessMethod` | A preprocess method character string.
`...` | For the constructor, additional arguments to be passed to `SummarizedExperiment`; of particular interest are `colData` and `metadata`. For `mapToGenome`, this is ignored.

### Details

This class holds `M` or `Beta` values (or both) together with associated genomic coordinates. It is not possible to get `Meth` or `Unmeth` values from this object. The intention is to use this kind of object as an analysis end point.

In case one of `M` or `Beta` is missing, the other is computed on the fly. For example, M is computed from Beta as the logit (base 2) of the Beta values.

### Value

An object of class `GenomicRatioSet` for the constructor.

### Constructor

Instances are constructed using the `GenomicRatioSet` function with the arguments outlined above.

### Accessors

A number of useful accessors are inherited from `RangedSummarizedExperiment`.

In the following code, `object` is a `GenomicRatioSet`.

`getBeta(object)`

  Get Beta, see details.

`getM(object)`

  get M-values, see details.

`getCN(object)`

  get copy number, see details.

`getManifest(object)`

  get the manifest associated with the object.

`sampleNames(object)`, `featureNames(object)`

  Get the sampleNames (colnames) or the featureNames (rownames).

`preprocessMethod(object)`, `annotation(object)`

  Get the preprocess method or annotation `character`.

### Utilities

`mapToGenome(object)`

  Since `object` is already mapped to the genome, this method simply returns `object` unchanged.

`combine`:

  Combines two different `GenomicRatioSet`, eventually using the `cbind` method for `SummarizedExperiment`.

### Author(s)

Kasper Daniel Hansen khansen@jhsph.edu

### See Also

`RangedSummarizedExperiment` in the SummarizedExperiment package for the basic class structure.

### Examples

      showClass("GenomicRatioSet")

[Package minfi version 1.38.0 Index]