BeadStudioSet-class {oligoClasses} | R Documentation

## Class `"BeadStudioSet"`

### Description

A container for log R ratios and B allele frequencies from SNP arrays.

### Objects from the Class

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

### Slots

`featureData`:

  Object of class `"GenomeAnnotatedDataFrame"` ~~

`assayData`:

  Object of class `"AssayData"` ~~

`phenoData`:

  Object of class `"AnnotatedDataFrame"` ~~

`experimentData`:

  Object of class `"MIAxE"` ~~

`annotation`:

  Object of class `"character"` ~~

`protocolData`:

  Object of class `"AnnotatedDataFrame"` ~~

`genome`:

  Object of class `"character"` ~~

`.__classVersion__`:

  Object of class `"Versions"` ~~

### Extends

Class `"gSet"`, directly. Class `"eSet"`, by class "gSet", distance 2. Class `"VersionedBiobase"`, by class "gSet", distance 3. Class `"Versioned"`, by class "gSet", distance 4.

### Methods

In the methods below, `object` has class `BeadStudioSet`.

  `baf(object)`: accessor for the matrix of B allele frequencies.

  `baf(object) <- value` replacement method for B allele frequencies: `value` must be a matrix of integers.

  `as(object, "data.frame")`: coerce to data.frame with column headers 'lrr', 'baf', 'x' (physical position with unit Mb), 'id', and 'is.snp'. Used for plotting with lattice.

  `copyNumber(object)`: accessor for log R ratios.

  `copyNumber(object) <- value`: replacement method for the log R ratios

initialize

  `signature(.Object = "BeadStudioSet")`: constructs an instance of the class

  `lrr(object)`: accessor for matrix of log R ratios

  `lrr(object) <- value` replacement method for log R ratios: `value` should be a matrix or a `ff_matrix`.

  `show(object)`: print a short summary of the `BeadStudioSet` object.

  `updateObject(object)`: update a `BeadStudioSet` object.

### Author(s)

R. Scharpf

### Examples

    new("BeadStudioSet")

[Package oligoClasses version 1.56.0 Index]