RatioSet-class: RatioSet instances

In hansenlab/minfi: Analyze Illumina Infinium DNA methylation arrays

RatioSet instances

Description

This class holds preprocessed data for Illumina methylation microarrays.

Usage

## Constructor

RatioSet(Beta = NULL, M = NULL, CN = NULL,
        annotation = "", preprocessMethod = "", ...)

## 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)
## S4 method for signature 'RatioSet'
annotation(object)
## S4 method for signature 'RatioSet'
pData(object)
## S4 method for signature 'RatioSet'
sampleNames(object)
## S4 method for signature 'RatioSet'
featureNames(object)

Arguments

object	A RatioSet.
Beta	A matrix of beta values (between zero and one) with each row being a methylation loci and each column a sample.
M	A matrix of log-ratios (between minus infinity and infinity) with each row being a methylation loci and each column a sample.
CN	An optional matrix of copy number estimates with each row being a methylation loci and each column a sample.
annotation	An annotation string, optional.
preprocessMethod	A character, optional.
...	For the constructor, additional arguments to be passed to SummarizedExperiment; of particular interest are colData, rowData and metadata. For getM these values gets passed onto getBeta.

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.

Value

An object of class RatioSet for the constructor.

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.

Utilities

In the following code, object is a RatioSet.

combine:

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

Author(s)

Kasper Daniel Hansen [e-mail]

See Also

eSet for the basic class structure. Objects of this class are typically created from an MethylSet using ratioConvert.

Examples

  showClass("RatioSet")

hansenlab/minfi documentation built on May 3, 2024, 3:49 p.m.