minfi (version 1.18.2)

RGChannelSet-class: 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"), ...)
RGChannelSetExtended(Green = new("matrix"), Red = new("matrix"),
                     GreenSD = new("matrix"), RedSD = new("matrix"),
                     NBeads = new("matrix"), ...)
## Accessors
## S3 method for class 'RGChannelSet':
getBeta(object, \dots)
getGreen(object)
getRed(object)
## S3 method for class '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.

...

Additional objects passes to the eSet constructor, particular a phenoData slot.

Constructors

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

See Also

See eSet 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")