Class "cghExSet" for combining CGH and expression data

Description

combination of an ExpressionSet and CGH assay results

Usage

make_cghExSet(exprs, logRatios, cloneMeta, pd, mi, anno) # pd is AnnotatedDataFrame, mi is MIAME

Arguments

Objects from the Class

Objects can be created by calls of the form new("cghExSet", phenoData, experimentData, annotation, exprs, logRatios, cloneMeta).

Slots

cghAssays:

Object of class "AssayData" rectangular representation of logRatio data from CGH

cloneMeta:

Object of class "AnnotatedDataFrame" information on chromosome and offset of clones

assayData:

Object of class "AssayData" expression assay results

phenoData:

Object of class "AnnotatedDataFrame" sample level data

featureData:

Object of class "AnnotatedDataFrame" reporter level metadata for expression assay results

experimentData:

Object of class "MIAME" container for experiment documentation

annotation:

Object of class "character" identifiers for expression and CGH platforms, as a named vector with elements named 'exprs' and 'logRatios'

.__classVersion__:

Object of class "Versions"

Extends

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

Methods

cloneMeta

signature(cghSet = "cghExSet"): extract annotated data frame on clone locations for CGH component

cloneNames

signature(cghSet = "cghExSet"): extract character vector of clone IDs for CGH component

exprs

signature(object = "cghExSet"): extract expression assay results

initialize

signature(.Object = "cghExSet"): infrastructure

logRatios

signature(cghSet = "cghExSet"): extract CGH assay results

show

signature(object = "cghExSet"): display object in concise form

Author(s)

V Carey <stvjc@channing.harvard.edu>

References

R. M. Neve Cancer Cell Dec 2006

Examples

showClass("cghExSet")
data(neveExCGH)
logRatios(neveExCGH)[1:4,]
exprs(neveExCGH)[1:4,]