| MultiSet {Biobase} | R Documentation |
Container for high-throughput assays and experimental
metadata. MutliSet is derived from
eSet-class. MultiSet differs from
ExpressionSet-class because MultiSet can contain
any element(s) in assayData (ExpressionSet must have an
element named exprs).
Directly extends class eSet.
new('MultiSet',
phenoData = [AnnotatedDataFrame],
experimentData = [MIAME],
annotation = [character],
...)
updateOldESet(oldESet,"MultiSet")
MultiSet instances are usually created through
new("MultiSet", ...). The ... arguments to new
are matrices of expression data (with features
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.
updateOldESet will take a serialized instance (e.g., saved to a disk
file with save object created with earlier definitions of
the eSet-class, and update the object to
MultiSet. Warnings are issued when direct translation is not
possible; incorrectly created oldESet instances may not be updated.
Inherited from eSet:
assayData:nrow(phenoData). Each matrix in assayData has rows
represening features (e.g., reporters) and columns representing
samples. Class:AssayData-classphenoData:eSet-classexperimentData:eSet-classannotation:eSet-classClass-specific methods: none
Derived from eSet-class:
updateObject(object, ..., verbose=FALSE)updateObject and eSetisCurrent(object)isCurrentisVersioned(object)isVersionedsampleNames(MultiSet) and sampleNames(MultiSet)<-:eSet-classfeatureNames(MultiSet), featureNames(MultiSet, value)<-:eSet-classdims(MultiSet):eSet-classphenoData(MultiSet), phenoData(MultiSet,value)<-:eSet-classvarLabels(MultiSet), varLabels(MultiSet, value)<-:eSet-classvarMetadata(MultiSet), varMetadata(MultiSet,value)<-:eSet-classpData(MultiSet), pData(MultiSet,value)<-:eSet-classvarMetadata(MultiSet), varMetadata(MultiSet,value)eSet-classexperimentData(MultiSet),experimentData(MultiSet,value)<-:eSet-classpubMedIds(MultiSet), pubMedIds(MultiSet,value)eSet-classabstract(MultiSet):eSet-classannotation(MultiSet), annotation(MultiSet,value)<-eSet-classcombine(MultiSet,MultiSet):eSet-classstorageMode(eSet), storageMode(eSet,character)<-:eSet-classreporterNames(MultiSet), reporterNames(MultiSet,value)<-:Standard generic methods:
initialize(MultiSet):new; not to be called directly by the user.validObject(MultiSet):assayData are matricies with equal dimensions.as(eSet,MultiSet):eSet portion of an object to MultiSet.show(MultiSet)eSet-classdim(MultiSet), ncoleSet-classMultiSet[(index):eSet-classMultiSet$, MultiSet$<-eSet-classBiocore team
eSet-class, ExpressionSet-class
# create an instance of ExpressionSet
new("MultiSet")
# update existing eSet class to MultiSet
data(sample.eSet)
multiSet <- as(sample.eSet,"MultiSet")
multiSet
# information about assay and sample data
featureNames(multiSet)[1:10]
sampleNames(multiSet)[1:5]
phenoData(multiSet)
experimentData(multiSet)