gSetList-class: Virtual Class for Lists of eSets

In benilton/oligoClassesOld: 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

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

benilton/oligoClassesOld documentation built on May 12, 2019, 11:51 a.m.