methylumi (version 2.18.2)

MethyLumiSet-class: Class "MethyLumiSet" for containing Illumina methylation data

Description

This class inherits from the MethyLumi class (and therefore, from eSet in Biobase) and is designed to hold both the intensities and the calculated betas, as well as pvalues if present.

Objects from the Class

Objects can be created by calls of the form new("MethyLumiSet", assayData, phenoData, featureData, experimentData, annotation, betas). An object of this type is the main storage class for methylation data from Illumina. Subsetting, etc., works as normal (rows represent genes, columns represent samples). There is also a rudimentary history tracking system that is modeled after that from the lumi package.

Extends

Class "MethyLumi", directly. Class "methylData", directly. Class "eSet", by class "MethyLumi", distance 2. Class "VersionedBiobase", by class "MethyLumi", distance 3. Class "Versioned", by class "MethyLumi", distance 4.

See Also

methylumiR, normalizeMethyLumiSet, methylumIDAT, MethyLumiQC, eSet

Examples

showClass("MethyLumiSet")