CopyNumberSet-class {oligoClasses} | R Documentation

## Class `"CopyNumberSet"`

### 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))

[Package oligoClasses version 1.50.4 Index]