CopyNumberSet-class: Class '"CopyNumberSet"'

In benilton/oligoClassesOld: Classes for high-throughput arrays supported by oligo and crlmm

Description

Container for storing total copy number estimates and confidence scores of the copy number estimates.

Objects from the Class

Objects can be created by calls of the form new("CopyNumberSet", assayData, phenoData, featureData, experimentData, annotation, protocolData, copyNumber, cnConfidence, ...).

Slots

assayData:

Object of class "AssayData" ~~

phenoData:

Object of class "AnnotatedDataFrame" ~~

featureData:

Object of class "AnnotatedDataFrame" ~~

experimentData:

Object of class "MIAxE" ~~

annotation:

Object of class "character" ~~

protocolData:

Object of class "AnnotatedDataFrame" ~~

.__classVersion__:

Object of class "Versions" ~~

Extends

Class "eSet", directly. Class "VersionedBiobase", by class "eSet", distance 2. Class "Versioned", by class "eSet", distance 3.

Methods

cnConfidence

signature(object = "CopyNumberSet"): ...

cnConfidence<-

signature(object = "CopyNumberSet", value = "matrix"): ...

coerce

signature(from = "CNSet", to = "CopyNumberSet"): ...

copyNumber

signature(object = "CopyNumberSet"): ...

copyNumber<-

signature(object = "CopyNumberSet", value = "matrix"): ...

initialize

signature(.Object = "CopyNumberSet"): ...

Note

This container is primarily for platforms for which genotypes are unavailable. As oligoSnpSet extends this class, methods related to total copy number that do not depend on genotypes can be defined at this level.

Author(s)

R. Scharpf

See Also

For genotyping platforms, total copy number estimates and genotype calls can be stored in the oligoSnpSet class.

Examples

showClass("CopyNumberSet")
cnset <- new("CopyNumberSet")
ls(Biobase::assayData(cnset))

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