RatioSet-class {minfi} | R Documentation

## RatioSet instances

### Description

This class holds preprocessed data for Illumina methylation microarrays.

### Usage

    ## Constructor

    RatioSet(Beta = NULL, M = NULL, CN = NULL,
            annotation = "", preprocessMethod = "", ...)

    ## Data extraction / Accessors

    ## S4 method for signature 'RatioSet'
    getBeta(object)
    ## S4 method for signature 'RatioSet'
    getM(object)
    ## S4 method for signature 'RatioSet'
    getCN(object)
    ## S4 method for signature 'RatioSet'
    preprocessMethod(object)
    ## S4 method for signature 'RatioSet'
    annotation(object)
    ## S4 method for signature 'RatioSet'
    pData(object)
    ## S4 method for signature 'RatioSet'
    sampleNames(object)
    ## S4 method for signature 'RatioSet'
    featureNames(object)

### Arguments

`object` | A `RatioSet`.
`Beta` | A matrix of beta values (between zero and one) with each row being a methylation loci and each column a sample.
`M` | A matrix of log-ratios (between minus infinity and infinity) with each row being a methylation loci and each column a sample.
`CN` | An optional matrix of copy number estimates with each row being a methylation loci and each column a sample.
`annotation` | An annotation string, optional.
`preprocessMethod` | A `character`, optional.
`...` | For the constructor, additional arguments to be passed to `SummarizedExperiment`; of particular interest are `colData`, `rowData` and `metadata`. For `getM` these values gets passed onto `getBeta`.

### Details

This class inherits from `eSet`. Essentially the class is a representation of a `Beta` matrix and/or a `M` matrix and optionally a `CN` (copy number) matrix linked to a `pData` data frame.

In addition, an annotation and a preprocessMethod slot is present. The annotation slot describes the type of array and also which annotation package to use. The preprocessMethod slot describes the kind of preprocessing that resulted in this dataset.

For a `RatioSet`, M-values are defined as `logit2` of the Beta-values if the M-values are not present in the object. Similarly, if only M-values are present in the object, Beta-values are `ilogit2` of the M-values.

### Value

An object of class `RatioSet` for the constructor.

### Constructor

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

### Accessors

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

`getBeta(object)`, `getM(object)`, `CN(object)`

  Get the Beta, M or CN matrix.

`getManifest(object)`

  get the manifest associated with the object.

`preprocessMethod(object)`

  Get the preprocess method `character`.

### Utilities

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

`combine`:

  Combines two different `RatioSet`, eventually using the `combine` method for `eSet`.

### Author(s)

Kasper Daniel Hansen khansen@jhsph.edu

### See Also

`eSet` for the basic class structure. Objects of this class are typically created from an `MethylSet` using `ratioConvert`.

### Examples

      showClass("RatioSet")

[Package minfi version 1.26.2 Index]