| SnpSetIllumina {beadarraySNP} | R Documentation |
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.
Directly extends class eSet.
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.
Inherited from Biobase:eSet:
assayData: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:AssayDataphenoData:eSetexperimentData:eSetannotation:eSetfeatureData:CHR and a MapInfo column for genomic localization Class-specific methods:
exprs(SnpSetIllumina), exprs(SnpSetIllumina,matrix)<-call in the AssayData
slot.combine(SnpSetIllumina,SnpSetIllumina):union-like
combination in both dimensions of SnpSetIllumina objectsreporterInfo(SnpSetIllumina), reporterInfo(SnpSetIllumina,matrix)<-pData in the featureData slot
Derived from eSet:
sampleNames(SnpSetIllumina) and sampleNames(SnpSetIllumina)<-:eSetfeatureNames(SnpSetIllumina), featureNames(SnpSetIllumina, value)<-:eSetdims(SnpSetIllumina):eSetphenoData(SnpSetIllumina), phenoData(SnpSetIllumina,value)<-:eSetvarLabels(SnpSetIllumina), varLabels(SnpSetIllumina, value)<-:eSetvarMetadata(SnpSetIllumina), varMetadata(SnpSetIllumina,value)<-:eSetpData(SnpSetIllumina), pData(SnpSetIllumina,value)<-:eSetvarMetadata(SnpSetIllumina), varMetadata(SnpSetIllumina,value)eSetexperimentData(SnpSetIllumina),experimentData(SnpSetIllumina,value)<-:eSetpubMedIds(SnpSetIllumina), pubMedIds(SnpSetIllumina,value)eSetabstract(SnpSetIllumina):eSetannotation(SnpSetIllumina), annotation(SnpSetIllumina,value)<-eSetstorageMode(eSet), storageMode(eSet,character)<-:eSetreporterNames(SnpSetIllumina), reporterNames(SnpSetIllumina,value)<-:featureData(SnpSetIllumina), featureData(SnpSetIllumina,AnnotatedDataFrame)<-eSetobject[(index):Standard generic methods:
initialize(SnpSetIllumina):new; not to be called directly by the user.validObject(SnpSetIllumina):call, callProbability, G, and R are members of
assayData. checkValidity(SnpSetIllumina) imposes this
validity check, and the validity checks of Biobase:eSet.show(SnpSetIllumina)eSetdim(SnpSetIllumina), ncoleSetSnpSetIllumina[(index):eSetSnpSetIllumina$, SnpSetIllumina$<-eSetJ. Oosting, based on Biobase eSet class