minfi (version 1.18.2)

RatioSet-class: RatioSet instances

Description

This class holds preprocessed data for Illumina methylation microarrays.

Usage

## Constructor
RatioSet(Beta = NULL, M = NULL, CN = NULL,  ...)
## Data extraction / Accessors
## S3 method for class 'RatioSet':
getBeta(object)
## S3 method for class 'RatioSet':
getM(object)
## S3 method for class 'RatioSet':
getCN(object)
## S3 method for class 'RatioSet':
preprocessMethod(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.

...

For the constructor: additional objects passes to the eSet constructor, particular a phenoData slot. For getM these values gets passed onto getBeta.

Constructor

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

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.

See Also

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

Examples

showClass("RatioSet")