IlluminaMethylationManifest-class {minfi} | 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 = new("DataFrame"),
                                TypeII = new("DataFrame"),
                                TypeControl = new("DataFrame"),
                                TypeSnpI = new("DataFrame"),
                                TypeSnpII = new("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.

### 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)

    }

[Package minfi version 1.30.0 Index]