MethyGenoSet-class {methyAnalysis} | R Documentation

## Class MethyGenoSet: contain and describe Illumina Infinium methylation data in GenoSet-class

### Description

This is a class representation for Illumina Infinium methylation microarray data. It directly extends `GenoSet`. The purpose of this class is to make the high-density methylation microarray data `MethyLumiM-class` compatible with the Biocoductor infrastructure packages designed for sequencing analysis.

### Extends

Directly extends class `GenoSet`.

### Creating Objects

MethyGenoSet(rowRanges, exprs, methylated, unmethylated, detection = NULL, pData = NULL, annotation = "", universe = NULL, assays=NULL, ...)

`MethyGenoSet` instances are usually created through converting from MethyLumiM object using MethyLumiM2GenoSet function or calling `MethyGenoSet` function as shown above. The arguments, rowRanges, exprs, methylated and unmethylated, are required; others can be missing. Please check `GenoSet` for more details of other parameters.

### Slots

`rowRanges`:

  a GRanges or RangedData object, inherited from `SummarizedExperiment`

`assays`:

  contains equal dimensional matrices: `exprs` (contains the methylation M-value, same as `MethyLumiM-class`), `methylated` (contains the methylated probe intensities. Same as `MethyLumiM-class`), `unmethylated` (contains the unmethylated probe intensities. Same as `MethyLumiM-class`), `detection` (records the detection p-value of the probe. Same as `MethyLumiM-class`). For more details of `assays`, please see `SummarizedExperiment`

`colData`:

  See `colData`

`annotation`:

  the annotation library of methylation data

`history`:

  a data.frame recording the operation history of the MethyGenoSet object.

### Methods

Class-specific methods:

`exprs(MethyGenoSet)`, `exprs(MethyGenoSet,matrix)<-`:

  Access and set elements named `exprs` in the `assays` slot.

`methylated(MethyGenoSet)`, `methylated(MethyGenoSet)<-`:

  Access and set elements named `methylated` in the `assays` slot.

`unmethylated(MethyGenoSet)`, `unjmethylated(MethyGenoSet)<-`:

  Access and set elements named `unmethylated` in the `assays` slot.

`detection(MethyGenoSet)`, `detection(MethyGenoSet)<-`:

  Access and set elements named `detection` in the `assays` slot.

`as(methyGenoSet,"MethyLumiM")`

  Coerce objects of `MethyGenoSet-class` to `MethyLumiM`

`as(genoSet,"MethyGenoSet")`

  Coerce objects of `GenoSet-class` to `MethyGenoSet`

`getHistory(MethyGenoSet)`:

  Access the operation history of `MethyGenoSet` object.

Derived from `GenoSet`:

`rowRanges(MethyGenoSet)`:

  return a GRanges object, which contains the chromosome location information

Derived from `SummarizedExperiment` (For the directly inherited methods, please see `GenoSet` and `SummarizedExperiment` ):

`combine(MethyGenoSet,missing)`:

  Combine two MethyGenoSet objects, including `history` slot

`exprs(MethyGenoSet)`, `exprs(MethyGenoSet,matrix)<-`:

  Access and set elements named `exprs` in the `assays` slot.

`object[(i,j)`:

  Conduct subsetting of the data in a MethyGenoSet object

Standard generic methods Please check see `GenoSet` and `SummarizedExperiment` for other inherited methods,

### Author(s)

Pan Du

### See Also

`MethyLumiM2GenoSet`)

### Examples

    ## load example data
    data(exampleMethyGenoSet)
    class(exampleMethyGenoSet)

[Package methyAnalysis version 1.26.0 Index]