RGChannelSet-class {minfi} | R Documentation

## Class `"RGChannelSet"`

### Description

These classes represents raw (unprocessed) data from a two color micro array; specifically an Illumina methylation array.

### Usage

    ## Constructors

    RGChannelSet(Green = new("matrix"), Red = new("matrix"),
                 annotation = "", ...)

    RGChannelSetExtended(Green = new("matrix"), Red = new("matrix"),
                        GreenSD = new("matrix"), RedSD = new("matrix"),
                        NBeads = new("matrix"), annotation = "", ...)

    ## Accessors

    ## S4 method for signature 'RGChannelSet'
    annotation(object)
    ## S4 method for signature 'RGChannelSet'
    pData(object)
    ## S4 method for signature 'RGChannelSet'
    sampleNames(object)
    ## S4 method for signature 'RGChannelSet'
    featureNames(object)
    ## S4 method for signature 'RGChannelSet'
    getBeta(object, ...)
    getGreen(object)
    getRed(object)
    getNBeads(object)
    ## S4 method for signature 'RGChannelSet'
    getManifest(object)

    ## Convenience functions
    getOOB(object)
    getSnpBeta(object)

### Arguments

`object` | An `RGChannelSet` (or `RGChannelSetExtended`).
`Green` | A matrix of Green channel values (between zero and infinity) with each row being a methylation loci and each column a sample.
`Red` | See the `Green` argument, but for the Green channel.
`GreenSD` | See the `Green` argument, but for standard deviations of the Green channel summaries.
`RedSD` | See the `Green`, but for standard deviations of the Red channel summaries.
`NBeads` | See the `Green` argument, but contains the number of beads used to summarize the Green and Red channels.
`annotation` | An annotation string, optional.
`...` | For the constructor(s), additional arguments to be passed to `SummarizedExperiment`; of particular interest are `colData`, `rowData` and `metadata`. For `getBeta` these values gets passed onto `getBeta`.

### Value

An object of class `RGChannelSet` or `RGChannelSetExtended` for the constructors.

### Constructors

Instances are constructed using the `RGChannelSet` or `RGChannelSetExtended` functions with the arguments outlined above.

`as(object, "RGChannelSet")` coerces a `RGChannelSetExtended` object into a `RGChannelSet`.

### Accessors

`getGreen`:

  Gets the Green channel as a matrix.

`getRed`:

  Gets the Red channel as a matrix.

`getNBeads`:

  Gets the number of beads as a matrix, this requires an `RGChannelSetExtended`.

`getManifest`:

  Gets the manifest object itself associated with the array type

### Convenience functions

`getOOB`:

  Retrives the so-called “out-of-band” (OOB) probes. These are the measurements of Type I probes in the “wrong” color channel. Return value is a list with two matrices, named `Red` and `Grn`.

`getSnpBeta`:

  Retrives the measurements of the 65 SNP probes located on the array. These SNP probes are intended to be used for sample tracking and sample mixups. The return value is a matrix of beta values. Each SNP probe ought to have values clustered around 3 distinct values corresponding to homo-, and hetero-zygotes.

`combine`:

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

### Tips

The class inherits a number of useful methods from `SummarizedExperiment`. In earliers versions of minfi, this class inherited from `eSet`, and we have kept of number of methods related to this, for example `pData`.

The best way to access phenotype data and sample names are `colData` and `colnames`.

Amongst the useful methods are

`dim`, `nrow`, `ncol`

  The dimension (number of probes by number of samples) of the experiment.

`colData`, `colnames`, `pData`, `sampleNames`

  Phenotype information and sample names.

`rownames`, `featureNames`

  This is the addresses (probe identifiers) of the array.

### Author(s)

Kasper Daniel Hansen khansen@jhsph.edu

### See Also

See `SummarizedExperiment` for the basic class that is used as a building block for `"RGChannelSet(Extended)"`. See `IlluminaMethylationManifest` for a class representing the design of the array.

### Examples

    showClass("RGChannelSet")

[Package minfi version 1.38.0 Index]