minfi (version 1.18.2)

IlluminaMethylationManifest-class: Class "IlluminaMethylationManifest"

Description

This is a class for representing an Illumina methylation microarray design, ie. the physical location and the probe sequences. This information should be independent of genome build and annotation.

Usage

## Constructor
IlluminaMethylationManifest(TypeI = new("DataFrame"),
                            TypeII = new("DataFrame"),
                            TypeControl = new("DataFrame"),
                            TypeSnpI = new("DataFrame"),
                            TypeSnpII = new("DataFrame"),
                            annotation = "")
## Data extraction
## S3 method for class 'IlluminaMethylationManifest':
getManifest(object)
## S3 method for class 'character':
getManifest(object)
getProbeInfo(object, type = c("I", "II", "Control",
                              "I-Green", "I-Red", "SnpI", "SnpII"))
getManifestInfo(object, type = c("nLoci", "locusNames"))
getControlAddress(object, controlType = c("NORM_A", "NORM_C",
                                          "NORM_G", "NORM_T"),
                  asList = FALSE)
getControlTypes(object)

Arguments

object

Either an object of class IlluminaMethylationManifest or class character for getManifest. For getProbeInfo, getManifestInfo and getControlAddress an object of either class RGChannelSet, IlluminaMethylationManifest.

TypeI

A DataFrame of type I probes.

TypeII

A DataFrame of type II probes.

TypeControl

A DataFrame of control probes.

TypeSnpI

A DataFrame of SNP type I probes.

TypeSnpII

A DataFrame of SNP type II probes.

annotation

An annotation character.

type

A single character describing what kind of information should be returned. For getProbeInfo it represents the following subtypes of probes on the array: Type I, Type II, Controls as well as Type I (methylation measured in the Green channel) and Type II (methylation measured in the Red channel). For getManifestInfo it represents either the number of methylation loci (approx. number of CpGs) on the array or the locus names.

controlType

A character vector of control types.

asList

If TRUE the return object is a list with one component for each controlType.

Details

The data slot contains the following objects: TypeI, TypeII and TypeControl which are all of class data.frame, describing the array design.

Methylation loci of type I are measured using two different probes, in either the red or the green channel. The columns AddressA, AddresB describes the physical location of the two probes on the array (with ProbeSeqA, ProbeSeqB giving the probe sequences), and the column Color describes which color channel is used.

Methylation loci of type II are measured using a single probe, but with two different color channels. The methylation signal is always measured in the green channel.

See Also

IlluminaMethylationAnnotation for annotation information for the array (information depending on a specific genome build).

Examples

if(require(IlluminaHumanMethylation450kmanifest)) {

show(IlluminaHumanMethylation450kmanifest)
head(getProbeInfo(IlluminaHumanMethylation450kmanifest, type = "I"))
head(IlluminaHumanMethylation450kmanifest@data$TypeI)
head(IlluminaHumanMethylation450kmanifest@data$TypeII)
head(IlluminaHumanMethylation450kmanifest@data$TypeControl)

}