minfi (version 1.18.2)

GenomicRatioSet-class: 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, pData = DataFrame(),
                annotation = "", preprocessMethod = "")
## Data extraction / Accessors
## S3 method for class 'GenomicRatioSet':
getBeta(object)
## S3 method for class 'GenomicRatioSet':
getM(object)
## S3 method for class 'GenomicRatioSet':
getCN(object)
## S3 method for class 'GenomicRatioSet':
pData(object)
## S3 method for class 'GenomicRatioSet':
sampleNames(object)
## S3 method for class 'GenomicRatioSet':
featureNames(object)
## S3 method for class 'GenomicRatioSet':
annotation(object)
## S3 method for class 'GenomicRatioSet':
preprocessMethod(object)
## S3 method for class 'GenomicRatioSet':
mapToGenome(object, \dots)

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.

pData

A DataFrame or data.frame object.

annotation

An annotation character string.

preprocessMethod

A preprocess method character string.

...

For mapToGenome, this is ignored.

Constructor

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

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.

See Also

RangedSummarizedExperiment in the SummarizedExperiment package for the basic class structure.

Examples

showClass("GenomicRatioSet")