Description Extends Creating Objects Slots Methods Author(s) See Also Examples
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],
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.
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
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
Biocore team
eSet-class
, ExpressionSet-class
1 2 | # create an instance of ExpressionSet
new("MultiSet")
|
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