shinyMethylSet-class: shinyMethylSet instances

Description Usage Arguments Details Constructor Accessors Author(s) See Also Examples

Description

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

Usage

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## 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

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  showClass("shinyMethylSet")

shinyMethyl documentation built on April 29, 2020, 5:28 a.m.