beadData-class {BeadExplorer}R Documentation

Class "beadData"

Description

A class to hold data information from a BeadChip experiment

Objects from the Class

Objects can be created by calls of the form new("beadData", ...).

Slots

fileOrigin:
Object of class "character": File paths of the data used to create the object
param:
Object of class "list": Parameters extracted from the source files
normMethod:
Object of class "character": The normalisation method applied to the object (if any)
detExprs:
Object of class "matrix": BeadStudio detection scores
exprs:
Object of class "exprMatrix": Unlogged intensity data
se.exprs:
Object of class "exprMatrix": Standard errors of bead replicates
description:
Object of class "character OR MIAME"
annotation:
Object of class "character": A name given to the analysis
notes:
Object of class "character": Notes
reporterInfo:
Object of class "data.frame Or NULL": reporter info
phenoData:
Object of class "phenoData": Phenotype data

Extends

Class "exprSet", directly. Class "annotatedDataset", by class "exprSet".

Methods

[
signature(x = "beadData"): subset for samples
boxplot
signature(x = "beadData"): boxplot of expression data
detectionCalls
signature(object = "beadData"): Obtain detection calls
detExprs
signature(object = "beadData"): slot accessor method
fileOrigin
signature(object = "beadData"): slot accessor method
nGenes
signature(object = "beadData"): Number of transcripts
normMethod
signature(object = "beadData"): slot accessor method
nSamples
signature(object = "beadData"): Number of samples
pairs
signature(x = "beadData"): Plot pairwise intensity plots
param
signature(object = "beadData"): slot accessor method
signalMeans
signature(object = "beadData"): Obtain signal means
summary
signature(object = "beadData"): Obtain summary of the data

Author(s)

Gareth Elvidge gareth.elvidge@well.ox.ac.uk

Examples

data(examplebeadData)
nGenes(examplebeadData)

[Package BeadExplorer version 1.2.0 Index]