BeadStudioSet-class: Class '"BeadStudioSet"'

In jmacdon/oligoClasses: Classes for high-throughput arrays supported by oligo and crlmm

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")

jmacdon/oligoClasses documentation built on Aug. 11, 2020, 12:32 a.m.