GenomicMethylSet-class {minfi} | R Documentation

## GenomicMethylSet instances

### Description

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

### Usage

    ## Constructor

    GenomicMethylSet(gr = GRanges(), Meth = new("matrix"),
                     Unmeth = new("matrix"), annotation = "",
                     preprocessMethod = "", ...)

    ## Data extraction / Accessors

    ## S4 method for signature 'GenomicMethylSet'
    getMeth(object)
    ## S4 method for signature 'GenomicMethylSet'
    getUnmeth(object)
    ## S4 method for signature 'GenomicMethylSet'
    getBeta(object, type = "", offset = 0, betaThreshold = 0)
    ## S4 method for signature 'GenomicMethylSet'
    getM(object, type = "", ...)
    ## S4 method for signature 'GenomicMethylSet'
    getCN(object, ...)
    ## S4 method for signature 'GenomicMethylSet'
    pData(object)
    ## S4 method for signature 'GenomicMethylSet'
    sampleNames(object)
    ## S4 method for signature 'GenomicMethylSet'
    featureNames(object)
    ## S4 method for signature 'GenomicMethylSet'
    annotation(object)
    ## S4 method for signature 'GenomicMethylSet'
    preprocessMethod(object)
    ## S4 method for signature 'GenomicMethylSet'
    mapToGenome(object, ...)

### Arguments

`object` | A `GenomicMethylSet`.
`gr` | A `GRanges` object.
`Meth` | A matrix of methylation values (between zero and infinity) with each row being a methylation loci and each column a sample.
`Unmeth` | See the `Meth` argument.
`annotation` | An annotation character string.
`preprocessMethod` | A preprocess method character string.
`type` | How are the values calculated? For `getBeta` setting `type="Illumina"` sets `offset=100` as per Genome Studio. For `getM` setting `type=""` computes M-values as the logarithm of `Meth`/`Unmeth`, otherwise it is computed as the logit of `getBeta(object)`.
`offset` | Offset in the beta ratio, see detail.
`betaThreshold` | Constrains the beta values to be in the inverval betwen `betaThreshold` and 1-`betaThreshold`.
`...` | For the constructor, additional arguments to be passed to `SummarizedExperiment`; of particular interest are `colData` and `metadata`. For `getM` these values gets passed onto `getBeta`. For `mapToGenome`, this is ignored.

### Details

For a detailed discussion of `getBeta` and `getM` see the deatils section of `MethylSet`.

### Value

An object of class `GenomicMethylSet` for the constructor.

### Constructor

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

### Accessors

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

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

`getMeth(object)`, `getUnmeth(object)`

  Get the Meth or Unmeth matrix.

`getBeta(object)`

  Get Beta, see details.

`getM(object)`

  get M-values, see details.

`getCN(object)`

  get copy number values which are defined as the sum of the methylation and unmethylation channel.

`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 `GenomicMethylSet`, 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. Objects of this class are typically created by using the function `mapToGenome` on a `MethylSet`.

### Examples

      showClass("GenomicMethylSet")

[Package minfi version 1.40.0 Index]