BeadLevelList-class {beadarray} | R Documentation

## Class "BeadLevelList"

### Description

A class for storing red and green channel foreground and background intensities from an Illumina experiment.

### Objects from the Class

Objects can be created by calls of the form `new("BeadLevelList")`, but are usually created by `readIllumina`.

### Slots/List Components

Objects of this class contain the following slots

`beadData`: | an environment for storing the raw bead-level data. Each row correspond to a bead and columns the data.
`phenoData`: | an 'AnnotatedDataFrame' containing experimental information.
`arrayInfo`: | a list containing array information.
`annotation`: | character storing annotation package information.
`beadAnno`: | a data.frame containing Bead annotation information.
`scanMetrics`: | a data.frame containing scanner information.

### Methods

show(BeadLevelList)
  printing method for BeadLevelList
initialize
  `signature(.Object = "BeadLevelList")`
dim
  `dim(object)`The dimension of the `BeadLevelList` object
`copyBeadLevelList(object)`
  Creates a new copy of a `BeadLevelList` object
`arrayNames(object,arrays=NULL)`
  Returns the strip/array names from a `BeadLevelList` object for selected `arrays`
`combineBeadLevelLists(object1,object2)`
  Combines two `BeadLevelList` objects into one
`getArrayData(object,what="G",log=TRUE)`
  Retrieves the `what` intensities on the `log` scale from the `BeadLevelList`
`numBeads(object,arrays=NULL)`
  Returns the number of beads on selected `arrays`
`pData(object)`
  Returns a data.frame with samples as rows, variables as columns
`phenoData(object)`
  Returns an object containing phenotypic information on both variable values and variable meta-data

### Author(s)

Mark Dunning and Matt Ritchie

### See Also

`readIllumina`

[Package beadarray version 1.8.0 Index]