MethyGenoSet-class: Class MethyGenoSet: contain and describe Illumina Infinium...

In methyAnalysis: DNA methylation data analysis and visualization

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 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)

methyAnalysis documentation built on Nov. 8, 2020, 8:09 p.m.