methylumi (version 2.18.2)

MethyLumi-class: The base class for storing Illumina Methylation data

Description

This class inherits from eSet from the Biobase package and is used as a base class for the other two methylumi classes, MethyLumiSet and MethyLumiQC.

Objects from the Class

The MethyLumi class is a virtual class and is not meant to be instantiated. Instead, one should instantiate a MethyLumiSet or a MethyLumiQC object.

Extends

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

See Also

methylumiR, MethyLumiSet, MethyLumiQC, eSet

Examples

## The class structure
showClass("MethyLumi")
## read in some data
## Read in sample information
samps <- read.table(system.file("extdata/samples.txt",
                                package = "methylumi"),sep="t",header=TRUE)
## Perform the actual data reading
## This is an example of reading data from a 
## Sentrix Array format file (actually two files,
## one for data and one for QC probes)
mldat <- methylumiR(system.file('extdata/exampledata.samples.txt',
        package='methylumi'),
      qcfile=system.file('extdata/exampledata.controls.txt',
        package="methylumi"),
      sampleDescriptions=samps)
mldat
## Get history information
getHistory(mldat)
## Get QC data, which is another eSet-derived object
QCdata(mldat)