gSetList-class: Virtual Class for Lists of eSets

In oligoClasses: Classes for high-throughput arrays supported by oligo and crlmm

Description

Virtual Class for Lists of eSets.

Objects from the Class

A virtual Class: No objects may be created from it.

Slots

assayDataList:

Object of class "AssayData" ~~

phenoData:

Object of class "AnnotatedDataFrame" ~~

protocolData:

Object of class "AnnotatedDataFrame" ~~

experimentData:

Object of class "MIAME" ~~

featureDataList:

Object of class "list" ~~

chromosome:

Object of class "vector" ~~

annotation:

Object of class "character" ~~

genome:

Object of class "character" ~~

Accessors

object is an instance of a gSetList-derived class.

annotation(object):

character string indicating the package used to provide annotation for the features on the array.

chromosome(object):

Returns the chromosome corresponding to each element in the gSetList object

elementNROWS(object): Returns the number of rows for each list of assays. In most gSetList-derived classes, the assays are organized by chromosome and elementNROWS returns the number of markers for each chromosome.

genomeBuild(object), genomeBuild(object) <- value:

Get or set the UCSC genome build. Supported builds are hg18 and hg19.

Coercion

object is an instance of a gSetList-derived class.

makeFeatureGRanges(object, ...):

Create a GRanges object for the featureData. The featureData is stored as a list. This method stacks the featureData from each list element. Metadata columns in the GRanges object include physical position ('position'), a SNP indicator ('isSnp'), and the chromosome. The genome build is extracted from object using the method genomeBuild.

Author(s)

R. Scharpf

See Also

oligoSetList, BeadStudioSetList

Examples

showClass("gSetList")

oligoClasses documentation built on Nov. 8, 2020, 5:32 p.m.