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")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(oligoClasses)
Welcome to oligoClasses version 1.34.0
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/oligoClasses/BeadStudioSet-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: BeadStudioSet-class
> ### Title: Class '"BeadStudioSet"'
> ### Aliases: BeadStudioSet-class BafLrrSet-class BeadStudioSet
> ###   baf,BeadStudioSet-method baf<-,BeadStudioSet-method baf<-
> ###   copyNumber,BeadStudioSet-method copyNumber<-,BeadStudioSet,ANY-method
> ###   coerce,BeadStudioSet,data.frame-method
> ###   initialize,BeadStudioSet-method lrr,BeadStudioSet-method
> ###   lrr<-,BeadStudioSet-method lrr<-,BeadStudioSet,ANY-method
> ###   lrr<-,BafLrrSet-method lrr<-,BafLrrSet,ANY-method lrr<-
> ###   show,BeadStudioSet-method updateObject,BeadStudioSet-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> new("BeadStudioSet")
BeadStudioSet (storageMode: lockedEnvironment)
assayData: 0 features, 0 samples 
  element names: baf, lrr 
protocolData: none
phenoData: none
featureData
  featureNames:
  fvarLabels: isSnp position chromosome
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
genome:   
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>