RGChannelSet-class: Class '"RGChannelSet"'

In hansenlab/minfi: Analyze Illumina Infinium DNA methylation arrays

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 [e-mail]

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")

hansenlab/minfi documentation built on Feb. 2, 2024, 11:23 a.m.