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 item stored in beadData is a data.frame which can be accessed by BLData[[1]]. Each row correspond to a bead and columns the data.
phenoData: an 'AnnotatedDataFrame' containing experimental information.
arrayInfo: a list containing array 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")
copyBeadLevelList(object)
Creates a new copy of a BeadLevelList object
arrayNames(object)
Returns the array names from a BeadLevelList object
combineBeadLevelLists(object1,object2)
Combines two BeadLevelList objects into one
getArrayData(object,which="G",log=TRUE)
Retrieves the which intensities on the log scale from the BeadLevelList
numBeads(object)
Returns the numbers of bead on each array
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

See Also

readIllumina


[Package beadarray version 1.4.0 Index]