AlleleSet-class {oligoClasses} | R Documentation

## Class "AlleleSet"

### Description

A class for storing the locus-level summaries of the normalized intensities

### Objects from the Class

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

### Slots

`assayData`:

  Object of class `"AssayData"` ~~

`phenoData`:

  Object of class `"AnnotatedDataFrame"` ~~

`featureData`:

  Object of class `"AnnotatedDataFrame"` ~~

`experimentData`:

  Object of class `"MIAME"` ~~

`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

allele

  `signature(object = "AlleleSet")`: extract allele specific summaries. For 50K (XBA and Hind) and 250K (Sty and Nsp) arrays, an additional argument (strand) must be used (allowed values: 'sense', 'antisense'.

bothStrands

  `signature(object = "AlleleSet")`: tests if data contains allele summaries on both strands for a given SNP.

bothStrands

  `signature(object = "SnpFeatureSet")`: tests if data contains allele summaries on both strands for a given SnpFeatureSet.

db

  `signature(object = "AlleleSet")`: link to database connection.

getA

  `signature(object = "AlleleSet")`: average intensities (across alleles)

getM

  `signature(object = "AlleleSet")`: log-ratio (Allele A vs. Allele B)

### Author(s)

R. Scharpf

### See Also

`SnpSuperSet`, `CNSet`

### Examples

    showClass("AlleleSet")
    ## an empty AlleleSet
    x <- new("matrix")
    new("AlleleSet", senseAlleleA=x, senseAlleleB=x, antisenseAlleleA=x, antisenseAlleleB=x)
    ##or
    new("AlleleSet", alleleA=x, alleleB=x)

[Package oligoClasses version 1.42.0 Index]