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]