| eSet {Biobase} | R Documentation |
Container for high-throughput assays and experimental
metadata. Classes derived from eSet contain one or more
identical-sized matricies as assayData elements. Derived
classes (e.g., ExpressionSet-class, SnpSet-class)
specify which elements must be present in the assayData slot.
eSet object cannot be instantiated directly; see the examples
for useage.
eSet is a virtual class, so instances cannot be created.
Objects created under previous definitions of eSet-class can be
coerced to classes derived based on eSet using updateOldESet.
Introduced in eSet:
assayData:nrow(phenoData). Class:AssayData-classphenoData:assayData)
phenotypes. Class: AnnotatedDataFrame-classfeatureData:assayData) unique to this experiment. Use
the annotation slot to efficiently reference feature data
common to the annotation package used in the experiment. Class:
AnnotatedDataFrame-classexperimentData:MIAME-classannotation:character.classVersion:Versions-class
Methods defined in derived classes (e.g., ExpressionSet-class,
SnpSet-class) may override the methods described here.
Class-specific methods:
sampleNames(object) and
sampleNames(object)<-value:assayData and phenoDatafeatureNames(object),
featureNames(object) <- value:assayData.dims(object):dim) or
column numbers (ncol), or dimensions of all memebers
(dims) of assayData.phenoData(object),
phenoData(object) <- value:phenoData.featureData(object),
featureData(object) <- value:featureData.varLabels(object), varLabels(eSet,
value)<-:phenoData.varMetadata(object),
varMetadata(object) <- value:phenoData.pData(object), pData(object) <- value:varMetadata(object),
varMetadata(eSet,value)pDataexperimentData(object),experimentData(object) <- value:description(object),description(object) <- value:exprSet. notes(object),notes(object) <- value:signature(object="eSet", value="list") Retrieve and set unstructured notes associated with eSet.
signature(object="eSet", value="character") As with
value="list", but append value to current list of notes.pubMedIds(object), pubMedIds(eSet,value)experimentData.abstract(object):experimentData.annotation(object),
annotation(object) <- valuepreproc(object),
preproc(object) <- value:signature(object="eSet",
value="list") Access and set preprocessing information
in the MIAME-class object associated with this
eSet.combine(eSet,eSet):eSet
objects. To be combined, eSets must have identical numbers of
featureNames, distinct sampleNames, and identical annotation.storageMode(object), storageMode(eSet,character)<-:assayData. Can be used to 'unlock' environments,
or to change between list and environment modes of
storing assayData.reporterNames(object), reporterNames(object) <-
value:featureNamesStandard generic methods:
initialize(object):validObject(object):phenoData rows match the number and names of
assayData columnsas(eSet, "ExpressionSet")"eSet" to instance of ExpressionSet-class, if possible.as(eSet, "MultiSet")"eSet" to instance of MultiSet-class, if possible.updateObject(object, ..., verbose=FALSE)updateObjectupdateObjectTo(object, template, ..., verbose=FALSE)template, if necessary. Usually call by class inheritance, rather than directly by the user. See updateObjectToisCurrent(object)isCurrentisVersioned(object)isVersionedshow(object)dim(object), ncoldim) or column numbers (ncol), of all
memebers (dims) of assayData.object[(index):object$name, object$name<-valuename column in phenoDataobject[[i]], object[[i]]<-valuei (character or numeric index) in phenoDataAdditional functions:
element from assayData slot of object.element in assayData slot of object to matrix valueelement in assayData slot of object to matrix valueassayData slot of objectupdateOldESeteSet
constructued using listOrEnv as assayData slot
(before May, 2006).Biocore team
Method use in ExpressionSet-class.
Related classes
AssayData-class, AnnotatedDataFrame-class, MIAME-class.
Derived classes
ExpressionSet-class, SnpSet-class.
To update objects from previous class versions, see updateOldESet.
# update previous eSet-like class oldESet to existing derived class
## Not run: updateOldESet(oldESet, "ExpressionSet")
# create a new, ad hoc, class, for personal use
# all methods outlined above are available automatically
setClass("MySet", contains="eSet")
new("MySet")
# Create a more robust class, with initialization and validation methods
# to ensure assayData contains specific matricies
setClass("TwoColorSet", contains="eSet")
setMethod("initialize", "TwoColorSet",
function(.Object,
phenoData = new("AnnotatedDataFrame"),
experimentData = new("MIAME"),
annotation = character(),
R = new("matrix"),
G = new("matrix"),
Rb = new("matrix"),
Gb = new("matrix"),
... ) {
callNextMethod(.Object,
phenoData = phenoData,
experimentData = experimentData,
annotation = annotation,
R=R, G=G, Rb=Rb, Gb=Gb,
...)
})
setValidity("TwoColorSet", function(object) {
assayDataValidMembers(assayData(object), c("R", "G", "Rb", "Gb"))
})
new("TwoColorSet")
# eSet objects cannot be instantiated directly, only derived objects
try(new("eSet"))
removeClass("MySet")
removeClass("TwoColorSet")
removeMethod("initialize", "TwoColorSet")