eSet contain one or more
identical-sized matrices 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 usage.
eSet is a virtual class, so instances cannot be created. Objects created under previous definitions of eSet-class can be
coerced to the current classes derived from eSet using
updateOldESet.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:characterprotocolData:assayData) phenotypes.
Class: AnnotatedDataFrame-class.__classVersion__:Versions object describing
the R and Biobase version numbers used to created the instance.
Intended for developer use.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.dimnames(object), dimnames(object) <-
value:rownames and colnames; access and set
feature and sample names.dims(object):dim) or
column numbers (ncol), or dimensions of all members
(dims) of assayData.phenoData(object),
phenoData(object) <- value:phenoData. Adding new columns to phenoData is often
more easily done with eSetObject[["columnName"]] <- value.pData(object), pData(object) <- value:pData is often
more easily done with eSetObject[["columnName"]] <- value.varMetadata(object),
varMetadata(eSet,value)pDatavarLabels(object), varLabels(eSet,
value)<-:phenoData.featureData(object),
featureData(object) <- value:featureData.fData(object), fData(object) <- value:fvarMetadata(object),
fvarMetadata(eSet,value)fDatafvarLabels(object),
fvarLabels(eSet, value)<-:featureData.assayData(object), assayData(object) <- value:signature(object = "eSet", value = "AssayData"): Access
and replace the AssayData slot of an
eSet instance. assayData returns a list or
environment; elements in assayData not accessible in other
ways (e.g., via exprs applied directly to the eSet)
can most reliably be accessed with, e.g., assayData(obj)[["se.exprs"]].experimentData(object),experimentData(object) <- value:description(object),description(object) <- value: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) <- valueprotocolData(object),
protocolData(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.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 phenoData. The ... argument can include
named variables (especially labelDescription) to be added
to varMetadata.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).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
.MySet <- setClass("MySet", contains="eSet")
.MySet()
# Create a more robust class, with constructor and validation methods
# to ensure assayData contains specific matricies
.TwoColorSet <- setClass("TwoColorSet", contains="eSet")
TwoColorSet <-
function(phenoData=AnnotatedDataFrame(), experimentData=MIAME(),
annotation=character(), R=new("matrix"), G=new("matrix"),
Rb=new("matrix"), Gb=new("matrix"), ...)
{
.TwoColorSet(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"))
})
TwoColorSet()
# eSet objects cannot be instantiated directly, only derived objects
try(new("eSet"))
removeClass("MySet")
removeClass("TwoColorSet")
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