AlleleSetIllumina-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. "AlleleSetIllumina" class is derived from "eSet" and requires matrices “intensity”, “theta”, and “SE” as assay data members

Objects from the Class

new("AlleleSetIllumina", ...)

new("AlleleSetIllumina", phenoData = [AnnotatedDataFrame], featureData = [AnnotatedDataFrame], experimentData = [MIAME], annotation = [character], intensity = [matrix], theta = [matrix], SE = [matrix], ...)

Most arguments are optional, however usually the arguments to new include at least “intensity”, “theta”, and “SE”. Note that several methods requires additional assayData, phenoData, or featureData entries

"AlleleSetIllumina" instances are usually created from "BeadSetIllumina" instances using createAlleleSet or from text-files using createAlleleSetFromFiles

Slots

Inherited from "eSet":

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 “intensity”, “theta”, and “SE”. May also include intensities “A” and “B” (see createAlleleSet), “call” (see callGenotypes), “ped.check” (see validateCallsPedigree), or any other suitable matrix

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 = "AlleleSetIllumina"): 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”

assignToAlleleSet(object,object1):

Used to assign data in object1 to corresponding features in object, given the phenoData are identical between the two

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

createAlleleSet, callGenotypes, preprocessBeadSet, BeadSetIllumina, MultiSet

Examples

showClass("AlleleSetIllumina")

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