methyAnalysis (version 1.12.2)

MethyGenoSet-class: Class MethyGenoSet: contain and describe Illumina Infinium methylation data in GenoSet-class

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(locData, exprs, methylated, unmethylated, detection = NULL, pData = NULL, annotation = "", universe = NULL, assayData=NULL, ...) MethyGenoSet instances are usually created through converting from MethyLumiM object using MethyLumiM2GenoSet function or calling MethyGenoSet function as shown above. The arguments, locData, exprs, methylated and unmethylated, are required; others can be missing. Please check GenoSet for more details of other parameters.

Slots

locData:

a GRanges or RangedData object, inherited from GenoSet

assayData:

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 assayData, please see ExpressionSet

featureData:

See eSet

phenoData:

See eSet

experimentData:

See eSet

protocolData:

See eSet

annotation:

See eSet

.__classVersion__:

See eSet

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 AssayData-class slot.

methylated(MethyGenoSet), methylated(MethyGenoSet)<-:

Access and set elements named methylated in the AssayData-class slot.

unmethylated(MethyGenoSet), unjmethylated(MethyGenoSet)<-:

Access and set elements named unmethylated in the AssayData-class slot.

detection(MethyGenoSet), detection(MethyGenoSet)<-:

Access and set elements named detection in the AssayData-class 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:

locData(MethyGenoSet):

return a RangedData object, which contains the chromosome location information

Derived from ExpressionSet (For the directly inherited methods, please see ExpressionSet and eSet):

combine(MethyGenoSet,missing):

Combine two MethyGenoSet objects, including history slot. See eSet

exprs(MethyGenoSet), exprs(MethyGenoSet,matrix)<-:

Access and set elements named exprs in the AssayData-class slot.

object[(i,j):

Conduct subsetting of the data in a MethyGenoSet object

Standard generic methods Please check ExpressionSet and eSet for other inherited methods,

See Also

MethyLumiM2GenoSet)

Examples

## load example data
data(exampleMethyGenoSet)
class(exampleMethyGenoSet)