RatioSet instances

Description

This class holds preprocessed data for Illumina methylation microarrays.

Usage

## Constructor

RatioSet(Beta = NULL, M = NULL, CN = NULL,  ...)

## 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)

Arguments

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.

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.

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")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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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/RatioSet-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: RatioSet-class
> ### Title: RatioSet instances
> ### Aliases: RatioSet-class RatioSet getBeta,RatioSet-method
> ###   getM,RatioSet-method getCN,RatioSet-method
> ###   preprocessMethod,RatioSet-method show,RatioSet-method
> ###   initialize,RatioSet-method
> 
> ### ** Examples
> 
>   showClass("RatioSet")
Class "RatioSet" [package "minfi"]

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

Extends: 
Class "eSet", directly
Class "VersionedBiobase", by class "eSet", distance 2
Class "Versioned", by class "eSet", distance 3
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>