shinyMethyl (version 1.6.2)

shinyMethylSet-class: 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"))
## Data extraction / Accessors

## S3 method for class 'shinyMethylSet':
getMeth(object)
## S3 method for class 'shinyMethylSet':
getUnmeth(object)
## S3 method for class 'shinyMethylSet':
getBeta(object)
## S3 method for class 'shinyMethylSet':
getM(object)
## S3 method for class 'shinyMethylSet':
getCN(object)
## S3 method for class 'shinyMethylSet':
pData(object)
## S3 method for class '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

Constructor

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

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.

See Also

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

Examples

showClass("shinyMethylSet")