MultiSet

Class to Contain and Describe High-Throughput Expression Level Assays.

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).

Keywords
classes
Extends

Directly extends class eSet.

Creating Objects

new('MultiSet', phenoData = [AnnotatedDataFrame], experimentData = [MIAME], annotation = [character], protocolData = [AnnotatedDataFrame], ...) 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, annotation, and protocolData. phenoData, experimentData, annotation, and protocolData 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.

Slots

Inherited from eSet:

assayData:
Contains zero or more matrices with equal dimensions, and with column number equal to nrow(phenoData). Each matrix in assayData has rows representing features (e.g., reporters) and columns representing samples. Class:AssayData-class
phenoData:
See eSet-class
experimentData:
See eSet-class
annotation:
See eSet-class
protocolData:
See eSet-class

Methods

Class-specific methods: none Derived from eSet-class:

updateObject(object, ..., verbose=FALSE)
Update instance to current version, if necessary. See updateObject and eSet
isCurrent(object)
Determine whether version of object is current. See isCurrent
isVersioned(object)
Determine whether object contains a 'version' string describing its structure . See isVersioned
sampleNames(MultiSet) and sampleNames(MultiSet)<-:
See eSet-class
featureNames(MultiSet), featureNames(MultiSet, value)<-:
See eSet-class
dims(MultiSet):
See eSet-class
phenoData(MultiSet), phenoData(MultiSet,value)<-:
See eSet-class
varLabels(MultiSet), varLabels(MultiSet, value)<-:
See eSet-class
varMetadata(MultiSet), varMetadata(MultiSet,value)<-:
See eSet-class
pData(MultiSet), pData(MultiSet,value)<-:
See eSet-class
varMetadata(MultiSet), varMetadata(MultiSet,value)
See eSet-class
experimentData(MultiSet),experimentData(MultiSet,value)<-:
See eSet-class
pubMedIds(MultiSet), pubMedIds(MultiSet,value)
See eSet-class
abstract(MultiSet):
See eSet-class
annotation(MultiSet), annotation(MultiSet,value)<-
See eSet-class
protocolData(MultiSet), protocolData(MultiSet,value)<-
See eSet-class
combine(MultiSet,MultiSet):
See eSet-class
storageMode(eSet), storageMode(eSet,character)<-:
See eSet-class
Standard generic methods:
initialize(MultiSet):
Object instantiation, used by new; not to be called directly by the user.
validObject(MultiSet):
Validity-checking method, ensuring that all elements of assayData are matricies with equal dimensions.
as(eSet,MultiSet):
Coerce the eSet portion of an object to MultiSet.
show(MultiSet)
See eSet-class
dim(MultiSet), ncol
See eSet-class
MultiSet[(index):
See eSet-class
MultiSet$, MultiSet$<-
See eSet-class

See Also

eSet-class, ExpressionSet-class

Aliases
  • class:MultiSet
  • MultiSet
  • MultiSet-class
  • initialize,MultiSet-method
  • coerce,eSet,MultiSet-method
Examples
# create an instance of ExpressionSet
new("MultiSet")
Documentation reproduced from package Biobase, version 2.26.0, License: Artistic-2.0

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