cghExSet-class {Neve2006}R Documentation

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

exprs matrix of expression assay results
logRatios matrix of aCGH assay results
cloneMeta AnnotatedDataFrame for aCGH clone descriptions
pd AnnotatedDataFrame for sample level data
mi MIAME instance for experiment documentation
anno character string with annotation platform descriptor for expression data

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,]

[Package Neve2006 version 0.1.6 Index]