GenomicRatioSet-class: GenomicRatioSet instances

In hansenlab/minfi: Analyze Illumina Infinium DNA methylation arrays

GenomicRatioSet instances

Description

This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic location.

Usage

## Constructor

GenomicRatioSet(gr = GRanges(), Beta = NULL, M = NULL,
                CN = NULL, annotation = "",
                preprocessMethod = "", ...)

## Data extraction / Accessors

## S4 method for signature 'GenomicRatioSet'
getBeta(object)
## S4 method for signature 'GenomicRatioSet'
getM(object)
## S4 method for signature 'GenomicRatioSet'
getCN(object)
## S4 method for signature 'GenomicRatioSet'
pData(object)
## S4 method for signature 'GenomicRatioSet'
sampleNames(object)
## S4 method for signature 'GenomicRatioSet'
featureNames(object)
## S4 method for signature 'GenomicRatioSet'
annotation(object)
## S4 method for signature 'GenomicRatioSet'
preprocessMethod(object)
## S4 method for signature 'GenomicRatioSet'
mapToGenome(object, ...)

Arguments

object	A GenomicRatioSet.
gr	A GRanges object.
Beta	A matrix of beta values (optional, see details).
M	A matrix of M values (optional, see details).
CN	A matrix of copy number values.
annotation	An annotation character string.
preprocessMethod	A preprocess method character string.
...	For the constructor, additional arguments to be passed to SummarizedExperiment; of particular interest are colData and metadata. For mapToGenome, this is ignored.

Details

This class holds M or Beta values (or both) together with associated genomic coordinates. It is not possible to get Meth or Unmeth values from this object. The intention is to use this kind of object as an analysis end point.

In case one of M or Beta is missing, the other is computed on the fly. For example, M is computed from Beta as the logit (base 2) of the Beta values.

Value

An object of class GenomicRatioSet for the constructor.

Constructor

Instances are constructed using the GenomicRatioSet function with the arguments outlined above.

Accessors

A number of useful accessors are inherited from RangedSummarizedExperiment.

In the following code, object is a GenomicRatioSet.

getBeta(object)

Get Beta, see details.

getM(object)

get M-values, see details.

getCN(object)

get copy number, see details.

getManifest(object)

get the manifest associated with the object.

sampleNames(object), featureNames(object)

Get the sampleNames (colnames) or the featureNames (rownames).

preprocessMethod(object), annotation(object)

Get the preprocess method or annotation character.

Utilities

mapToGenome(object)

Since object is already mapped to the genome, this method simply returns object unchanged.

combine:

Combines two different GenomicRatioSet, eventually using the cbind method for SummarizedExperiment.

Author(s)

Kasper Daniel Hansen [e-mail]

See Also

RangedSummarizedExperiment in the SummarizedExperiment package for the basic class structure.

Examples

  showClass("GenomicRatioSet")

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