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-class
phenoData
:eSet-class
experimentData
:eSet-class
annotation
:eSet-class
Class-specific methods: none
Derived from eSet-class
:
sampleNames(MultiSet)
and sampleNames(MultiSet)<-
:eSet-class
featureNames(MultiSet)
, featureNames(MultiSet, value)<-
:eSet-class
dims(MultiSet)
:eSet-class
phenoData(MultiSet)
, phenoData(MultiSet,value)<-
:eSet-class
varLabels(MultiSet)
, varLabels(MultiSet, value)<-
:eSet-class
varMetadata(MultiSet)
, varMetadata(MultiSet,value)<-
:eSet-class
pData(MultiSet)
, pData(MultiSet,value)<-
:eSet-class
varMetadata(MultiSet)
, varMetadata(MultiSet,value)
eSet-class
experimentData(MultiSet)
,experimentData(MultiSet,value)<-
:eSet-class
pubMedIds(MultiSet)
, pubMedIds(MultiSet,value)
eSet-class
abstract(MultiSet)
:eSet-class
annotation(MultiSet)
, annotation(MultiSet,value)<-
eSet-class
combine(MultiSet,MultiSet)
:eSet-class
storageMode(eSet)
, storageMode(eSet,character)<-
:eSet-class
reporterNames(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.show(MultiSet)
eSet-class
dim(MultiSet)
, ncol
eSet-class
MultiSet[(index)
:eSet-class
MultiSet$
, MultiSet$<-
eSet-class
Biocore team
eSet-class
, ExpressionSet-class
# create an instance of ExpressionSet new("ExpressionSet") # update existing exprSet-like class to ExpressionSet data(sample.exprSet) expressionSet <- as(sample.exprSet,"ExpressionSet") expressionSet # information about assay and sample data featureNames(expressionSet)[1:10] sampleNames(expressionSet)[1:5] phenoData(expressionSet) experimentData(expressionSet) # subset: first 10 genes, samples 2, 4, and 10 expressionSet <- as(sample.exprSet,"ExpressionSet") expressionSet[1:10,c(2,4,10)] # named features and their expression levels subset <- expressionSet[c("AFFX-BioC-3_at","AFFX-BioDn-5_at"),] exprs(subset) # samples with above-average 'score' in phenoData highScores <- expressionSet$score > mean(expressionSet$score) expressionSet[,highScores]