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.

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 1.10.0 Index]