BeadSetIllumina-class: Class to Contain Objects Describing High-Throughput Illumina...

In beadarrayMSV: Analysis of Illumina BeadArray SNP data including MSV markers

Description

Container for high-throughput assays and experimental metadata. "BeadSetIllumina" class is derived from "eSet" and requires matrices “R”, “G”, “se.R”, “se.G”, and “no.beads” as assay data members

Objects from the Class

new("BeadSetIllumina", ...)

new("BeadSetIllumina", phenoData = [AnnotatedDataFrame], featureData = [AnnotatedDataFrame], experimentData = [MIAME], annotation = [character], R = [matrix], G = [matrix], se.R = [matrix], se.G = [matrix], no.beads = [matrix], ...)

"BeadSetIllumina" instances are usually created from bead type summary text-files using readBeadSummaryOutput

Slots

assayData:

Object of class "AssayData", with storage mode “list”. Contains data-matrices with rows corresponding to markers and columns to samples/arrays. Required members are “R”, “G”, “se.R”, “se.G”, and “no.beads”.

phenoData:

Object of class "AnnotatedDataFrame" with additional information about the samples.

featureData:

Object of class "AnnotatedDataFrame" with additional information about the markers.

experimentData:

Object of class "MIAME"

annotation:

Object of class "character"

.__classVersion__:

Object of class "Versions"

Extends

Class "eSet", directly. Class "VersionedBiobase", by class "eSet", distance 2. Class "Versioned", by class "eSet", distance 3.

Methods

Class-specific methods:

initialize

signature(.Object = "BeadSetIllumina"): Object instantiation, can be called by derived classes but not usually by the user.

validObject(object):

Validity-checking method, ensuring (1) all assayData components have the same number and names of features and samples; (2) the number and names of phenoData and featureData rows match the number and names of assayData columns and rows, respectively; (3) storageMode(object) is set to “list”

A selection of methods inherited from "eSet":

sampleNames(object), sampleNames(object) <- value:

See "eSet"

featureNames(object), featureNames(object) <- value:

See "eSet"

phenoData(object), phenoData(object) <- value:

See "eSet"

pData(object), pData(object) <- value:

See "eSet"

varMetadata(object)

See "eSet"

varLabels(object)

See "eSet"

featureData(object), featureData(object) <- value:

See "eSet"

fData(object), fData(object) <- value:

See "eSet"

fvarMetadata(object)

See "eSet"

fvarLabels(object)

See "eSet"

assayData(object), assayData(object) <- value:

See "eSet"

combine(object,object1):

See "eSet"

storageMode(object):

See "eSet". Do not assign new values to storageMode, as this could render the object invalid

Author(s)

Lars Gidskehaug

See Also

readBeadSummaryOutput, preprocessBeadSet, createAlleleSet, AlleleSetIllumina, eSet

Examples

showClass("BeadSetIllumina")

beadarrayMSV documentation built on May 1, 2019, 6:33 p.m.