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

## S4 method for signature 'RGChannelSet'
getBeta(object, ...)
getGreen(object)
getRed(object)
## S4 method for signature 'RGChannelSet'
getManifest(object)

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

Arguments

Constructors

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

Accessors

getGreen:

Gets the Green channel as a matrix.

getRed:

Gets the Red channel as a matrix.

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.

Tips

The class inherits a number of useful methods from eSet. Amongst these are

dim, nrow, ncol

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

pData, sampleNames

Phenotype information and sample names.

featureNames

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

Author(s)

Kasper Daniel Hansen khansen@jhsph.edu

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")

Results

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> library(minfi)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: lattice
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biostrings
Loading required package: XVector
Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/minfi/RGChannelSet-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: RGChannelSet-class
> ### Title: Class '"RGChannelSet"'
> ### Aliases: RGChannelSet-class RGChannelSetExtended-class RGChannelSet
> ###   RGChannelSetExtended show,RGChannelSet-method
> ###   initialize,RGChannelSet-method initialize,RGChannelSetExtended-method
> ###   getBeta,RGChannelSet-method getManifest,RGChannelSet-method getGreen
> ###   getRed getOOB getSnpBeta
> 
> ### ** Examples
> 
> showClass("RGChannelSet")
Class "RGChannelSet" [package "minfi"]

Slots:
                                                               
Name:           assayData          phenoData        featureData
Class:          AssayData AnnotatedDataFrame AnnotatedDataFrame
                                                               
Name:      experimentData         annotation       protocolData
Class:              MIAxE          character AnnotatedDataFrame
                         
Name:   .__classVersion__
Class:           Versions

Extends: 
Class "eSet", directly
Class "VersionedBiobase", by class "eSet", distance 2
Class "Versioned", by class "eSet", distance 3

Known Subclasses: "RGChannelSetExtended"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>