SnpSetIllumina: Class to Contain Objects Describing High-Throughput SNP Assays.

Description

Container for high-throughput assays and experimental metadata. SnpSetIllumina class is derived from eSet, and requires matrices R, G, call, callProbability as assay data members.

It supports featureData. Several visualization methods use columns CHR and MapInfo. The CHR column is used to handle sex chromosomes in a specific way. The OPA column is the default way to specify subsamples.

Arguments

Extends

Directly extends class eSet.

Creating Objects

new('SnpSetIllumina',
    phenoData = [AnnotatedDataFrame],
    experimentData = [MIAME],
    annotation = [character],
    call = [matrix],
    callProbability = [matrix],
    G = [matrix],
    R = [matrix],
    featureData = [data.frameOrNULL],
    ...)

SnpSetIllumina instances are usually created through new("SnpSetIllumina", ...). Arguments to new include call (a matrix of gentoypic calls, with features (SNPs) corresponding to rows and samples to columns), callProbability, G, R, phenoData, experimentData, and annotation. phenoData, experimentData, and annotation can be missing, in which case they are assigned default values.

Slots

Inherited from Biobase:eSet:

assayData:: Contains matrices with equal dimensions, and with column number equal to nrow(phenoData). assayData must contain a matrix call with rows representing features (e.g., SNPs) and columns representing samples, a matrix callProbability describing the certainty of the call, and matrices R and G to describe allele specific intensities. The contents of these matrices are not enforced by the class. The assayData matrices Gb, Rb, intensity, theta are optional, but are either results or input for several methods of the class. Additional matrices of identical size may also be included in assayData. Class:AssayData.
phenoData:: See eSet.
experimentData:: See eSet.
annotation:: See eSet.
featureData:: annotation for SNPs, usually will contain a CHR and a MapInfo column for genomic localization.

Methods

Class-specific methods:

exprs(SnpSetIllumina), exprs(SnpSetIllumina,matrix)<-: Access and set elements named call in the AssayData slot.
combine(SnpSetIllumina,SnpSetIllumina):: performs union-like combination in both dimensions of SnpSetIllumina objects.
fData(SnpSetIllumina), fData(SnpSetIllumina,data.frame)<-: Access and set the pData in the featureData slot.
calculateGSR(SnpSetIllumina): calculate ratio of Gentrain score and Gencall score. Creates GSR matrix in assayData. Should be performed before combining datasets.
calculateSmooth(object,smoothType): calculate smoothed data, creates smoothed matrix in assayData. smoothType can only be "quantsmooth" at the moment
sortGenomic(SnpSetIllumina): order the data by chromosome and position on the chromosome.

Derived from eSet:

sampleNames(SnpSetIllumina) and sampleNames(SnpSetIllumina)<-:: See eSet.
featureNames(SnpSetIllumina), featureNames(SnpSetIllumina, value)<-:: See eSet.
dims(SnpSetIllumina):: See eSet.
phenoData(SnpSetIllumina), phenoData(SnpSetIllumina,value)<-:: See eSet.
varLabels(SnpSetIllumina), varLabels(SnpSetIllumina, value)<-:: See eSet.
varMetadata(SnpSetIllumina), varMetadata(SnpSetIllumina,value)<-:: See eSet.
pData(SnpSetIllumina), pData(SnpSetIllumina,value)<-:: See eSet.
varMetadata(SnpSetIllumina), varMetadata(SnpSetIllumina,value): See eSet.
experimentData(SnpSetIllumina),experimentData(SnpSetIllumina,value)<-:: See eSet.
pubMedIds(SnpSetIllumina), pubMedIds(SnpSetIllumina,value): See eSet.
abstract(SnpSetIllumina):: See eSet.
annotation(SnpSetIllumina), annotation(SnpSetIllumina,value)<-: See eSet.
storageMode(eSet), storageMode(eSet,character)<-:: See eSet.
featureData(SnpSetIllumina), featureData(SnpSetIllumina,AnnotatedDataFrame)<-: See eSet.
object[(index):: Conducts subsetting of matrices and phenoData and featureData components.

Standard generic methods: