shinyMethylSet-class {shinyMethyl} | R Documentation

## shinyMethylSet instances

### Description

This class holds summarized data from Illumina methylation microarrays for interactive visualization purpose.

### Usage

    ## Constructor

    shinyMethylSet(sampleNames = new("character"),
                   phenotype = new("data.frame"),
                   mQuantiles = new(vector("list",5)),
                   betaQuantiles = new(vector("list",5)),
                   methQuantiles = new(vector("list",5)),
                   unmethQuantiles = new(vector("list",5)),
                   cnQuantiles = new(vector("list",5)),
                   greenControls = new(vector("list",12)),
                   redControls = new(vector("list",12)),
                   pca = new("list"),
                   originObject = new("character"),
                   array = new("character"))

    ## Data extraction / Accessors

    ## S4 method for signature 'shinyMethylSet'
    getMeth(object)
    ## S4 method for signature 'shinyMethylSet'
    getUnmeth(object)
    ## S4 method for signature 'shinyMethylSet'
    getBeta(object)
    ## S4 method for signature 'shinyMethylSet'
    getM(object)
    ## S4 method for signature 'shinyMethylSet'
    getCN(object)
    ## S4 method for signature 'shinyMethylSet'
    pData(object)
    ## S4 method for signature 'shinyMethylSet'
    sampleNames(object)

### Arguments

`object` | A `shinyMethylSet`.
`sampleNames` | A character vector
`phenotype` | A `data.frame` object.
`methQuantiles` | A list of 5 matrices containing several quantiles for the methylation values (between zero and infinity) separated by probe tpye and autosomal/sex probes. Each row is a quantile and each column is a sample.
`unmethQuantiles` | Similar to `Meth`
`betaQuantiles` | Similar to `Meth` but for Beta-values
`mQuantiles` | Similar to `Meth` but for M-values
`cnQuantiles` | Similar to `Meth` but for Copy Number
`greenControls` | A list containing the matrices of different raw control probes intensities in the green channel
`redControls` | Similar to `greenControls` but for the red channel
`pca` | List containing the PCA scores for the 20,000 most variable CpGs and the percentages of variance explained
`originObject` | Name of the minfi object from which the data were extracted
`array` | Name of the Illumina array platform: 450k or EPIC

### Details

These class is a representation of a `Meth` matrix and a `Unmeth` matrix linked to a `pData` data frame.

A creationMethod slot is present to indicate from which object type the `shinyMethylSet` has been created: either a `RGChannelSet` or `GenomicRatioSet`

A `MethylSet` stores `meth` and `Unmeth`.

### Constructor

Instances are constructed using the `shinyMethylSet` function with the arguments outlined above.

### Accessors

In the following code, `object` is a `shinyMethylSet`.

`getMeth(object)`, `getUnmeth(object)`

  Get the Meth or Unmeth matrix.

`getBeta(object)`

  get Beta, see details.

`getM(object)`

  get M-values, see details.

`getCN(object)`

  get copy number values which are defined as the sum of the methylation and unmethylation channel.

`sampleNames(object)`

  Get the sampleNames

`combine(object1,object2)`

  combine `shinyMethylSet` objects

### Author(s)

Jean-Philippe Fortin jfortin@jhsph.edu

### See Also

Objects of this class are typically created by using the function `shinySummarize` on a `RGChannelSet` or `GenomicRatioSet`.

### Examples

      showClass("shinyMethylSet")

[Package shinyMethyl version 1.26.0 Index]