shinyMethylSet-class: shinyMethylSet instances
In Jfortin1/shinyMethyl: Interactive visualization for Illumina methylation arrays

shinyMethylSet-class

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