ExpressionSet {Biobase} | R Documentation |
Container for high-throughput assays and experimental
metadata. ExpressionSet
class is derived from
eSet
, and requires a matrix named exprs
as
assayData member.
Directly extends class eSet
.
new('ExpressionSet',
phenoData = [AnnotatedDataFrame],
experimentData = [MIAME],
annotation = [character],
exprs = [matrix],
...)
as([exprSet],"ExpressionSet")
ExpressionSet
instances are usually created through
new("ExpressionSet", ...)
. Usually the arguments to new
include exprs
(a matrix 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.
Inherited from eSet
:
assayData
:nrow(phenoData)
. assayData
must contain a matrix
exprs
with rows represening features (e.g., reporters)
and columns representing samples. Additional matrices of
identical size (e.g., representing measurement errors) may
also be included in assayData
. Class:AssayData-class
phenoData
:eSet
experimentData
:eSet
annotation
:eSet
Class-specific methods.
as(exprSet,"ExpressionSet")
exprSet-class
to ExpressionSet
exprs(ExpressionSet)
, exprs(ExpressionSet,matrix)<-
exprs
in the AssayData-class
slot.
Derived from eSet
:
sampleNames(ExpressionSet)
and sampleNames(ExpressionSet)<-
:eSet
featureNames(ExpressionSet)
, featureNames(ExpressionSet, value)<-
:eSet
dims(ExpressionSet)
:eSet
phenoData(ExpressionSet)
, phenoData(ExpressionSet,value)<-
:eSet
varLabels(ExpressionSet)
, varLabels(ExpressionSet, value)<-
:eSet
varMetadata(ExpressionSet)
, varMetadata(ExpressionSet,value)<-
:eSet
pData(ExpressionSet)
, pData(ExpressionSet,value)<-
:eSet
varMetadata(ExpressionSet)
, varMetadata(ExpressionSet,value)
eSet
experimentData(ExpressionSet)
,experimentData(ExpressionSet,value)<-
:eSet
pubMedIds(ExpressionSet)
, pubMedIds(ExpressionSet,value)
eSet
abstract(ExpressionSet)
:eSet
annotation(ExpressionSet)
, annotation(ExpressionSet,value)<-
eSet
combine(ExpressionSet,ExpressionSet)
:eSet
storageMode(eSet)
, storageMode(eSet,character)<-
:eSet
reporterNames(ExpressionSet)
, reporterNames(ExpressionSet,value)<-
:Standard generic methods:
initialize(ExpressionSet)
:new
; not to be called directly by the user.validObject(ExpressionSet)
:exprs
is a member of
assayData
. checkValidity(ExpressionSet)
imposes this
validity check, and the validity checks of eSet
.show(ExpressionSet)
eSet
dim(ExpressionSet)
, ncol
eSet
ExpressionSet[(index)
:eSet
ExpressionSet$
, ExpressionSet$<-
eSet
Biocore team
eSet-class
, ExpressionSet-class
# create an instance of ExpressionSet new("ExpressionSet") # update existing exprSet-like class to ExpressionSet data(sample.exprSet) expressionSet <- as(sample.exprSet,"ExpressionSet") expressionSet # information about assay and sample data featureNames(expressionSet)[1:10] sampleNames(expressionSet)[1:5] phenoData(expressionSet) experimentData(expressionSet) # subset: first 10 genes, samples 2, 4, and 10 expressionSet <- as(sample.exprSet,"ExpressionSet") expressionSet[1:10,c(2,4,10)] # named features and their expression levels subset <- expressionSet[c("AFFX-BioC-3_at","AFFX-BioDn-5_at"),] exprs(subset) # samples with above-average 'score' in phenoData highScores <- expressionSet$score > mean(expressionSet$score) expressionSet[,highScores]