Class "beadLevelData"

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("beadLevelData"), but are usually created by readIllumina.

Slots/List Components

Objects of this class contain the following slots

beadData: A list of arrays, indexed by array name. Each item in this list is itself a list, containing enviroments holding the data for that array.
sectionData: a list containing information. Each item in the list is a data frame containing one row for each section
experimentData: a list containing the annotation of the platform, link to the sdf file and type of data (slide or Sentrix Array Matrix)
history: Character vector storing the operations performed on this object.

Methods

show(beadLevelData)

Printing method for BeadLevelList

sectionNames(object,arrays=NULL)

Returns the strip/array names from a

numBeads(object,arrays=NULL)

Returns the number of beads on selected arrays

Accessing data from the class

getBeadData

retrieve data

insertBeadData

Input or modify existing data

Author(s)

Mark Dunning, Mike Smith

See Also

readIllumina

Examples

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if(require(beadarrayExampleData)){


data(exampleBLData)

sectionNames(exampleBLData)

head(exampleBLData[[1]])

getBeadData(exampleBLData, array=1, what="Grn")[1:10]


}

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