IlluminaMethylationManifest-class: Class '"IlluminaMethylationManifest"'
In hansenlab/minfi: Analyze Illumina Infinium DNA methylation arrays

IlluminaMethylationManifest-class

R Documentation

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 = DataFrame(),
                            TypeII = DataFrame(),
                            TypeControl = DataFrame(),
                            TypeSnpI = DataFrame(),
                            TypeSnpII = DataFrame(),
                            annotation = "")

## Data extraction
## S4 method for signature 'IlluminaMethylationManifest'
getManifest(object)
## S4 method for signature '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)

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`.

Value

An object of class IlluminaMethylationManifest for the constructor.

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.

Utilities

In the following code, object is a IlluminaMethylationManifest.

getManifest(object): Get the manifest object.
getProbeInfo(object): Returns a DataFrame giving the type I, type II or control probes. It is also possible to get the type I probes measured in the Green or Red channel. This function ensures that the return object only contains probes which are part of the input object. In case of a RGChannelSet and type I probes, both addresses needs to be in the object.
getManifestInfo(object): Get some information about the manifest object (the chip design).
getControlAddress(object): Get the control addresses for control probes of a certain type.
getControlTypes(object): Returns the types and the numbers of control probes of each type.

Author(s)

Kasper Daniel Hansen khansen@jhsph.edu.

Examples

if(require(IlluminaHumanMethylation450kmanifest)) {

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

}

hansenlab/minfi documentation built on May 3, 2024, 3:49 p.m.