| SnpSet {Biobase} | R Documentation |
Container for high-throughput assays and experimental
metadata. SnpSet class is derived from
eSet, and requires matricies call,
callProbability as assay data members.
Directly extends class eSet.
new('SnpSet',
phenoData = [AnnotatedDataFrame],
experimentData = [MIAME],
annotation = [character],
call = [matrix],
callProbability = [matrix],
...)
SnpSet instances are usually created through
new("SnpSet", ...). Usually the arguments to new
include call (a matrix of gentoypic calls, with features (SNPs)
corresponding to rows and samples to columns), phenoData,
experimentData, and annotation.
phenoData, experimentData, and annotation can be
missing, in which case they are assigned default values.
Inherited from eSet:
assayData:nrow(phenoData). assayData must contain a matrix
call with rows represening features (e.g., SNPs)
and columns representing samples, and a matrix
callProbability describing the certainty of the
call. The content of call and callProbability are
not enforced by the class. Additional matrices of
identical size may also be included in
assayData. Class:AssayData-classphenoData:eSetexperimentData:eSetannotation:eSetClass-specific methods:
exprs(SnpSet), exprs(SnpSet,matrix)<-call in the AssayData
slot.
Derived from eSet:
updateObject(object, ..., verbose=FALSE)updateObject and eSetisCurrent(object)isCurrentisVersioned(object)isVersionedsampleNames(SnpSet) and sampleNames(SnpSet)<-:eSetfeatureNames(SnpSet), featureNames(SnpSet, value)<-:eSetdims(SnpSet):eSetphenoData(SnpSet), phenoData(SnpSet,value)<-:eSetvarLabels(SnpSet), varLabels(SnpSet, value)<-:eSetvarMetadata(SnpSet), varMetadata(SnpSet,value)<-:eSetpData(SnpSet), pData(SnpSet,value)<-:eSetvarMetadata(SnpSet), varMetadata(SnpSet,value)eSetexperimentData(SnpSet),experimentData(SnpSet,value)<-:eSetpubMedIds(SnpSet), pubMedIds(SnpSet,value)eSetabstract(SnpSet):eSetannotation(SnpSet), annotation(SnpSet,value)<-eSetcombine(SnpSet,SnpSet):eSetstorageMode(eSet), storageMode(eSet,character)<-:eSetStandard generic methods:
initialize(SnpSet):new; not to be called directly by the user.validObject(SnpSet):call and callProbability is a member of assayData. checkValidity(SnpSet) imposes this validity check, and the validity checks of eSet.show(SnpSet)eSetdim(SnpSet), ncoleSetSnpSet[(index):eSetSnpSet$, SnpSet$<-eSetV.J. Carey, after initial design by R. Gentleman