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]