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-class
phenoData
:assayData
)
phenotypes.Class: AnnotatedDataFrame-class
experimentData
:MIAME-class
annotation
:character
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 phenoData
featureNames(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
.varLabels(object)
, varLabels(eSet,
value)<-
:phenoData
.varMetadata(object)
,
varMetadata(object) <- value
:phenoData
.pData(object)
, pData(object) <- value
:varMetadata(object)
,
varMetadata(eSet,value)
pData
experimentData(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
.pubMedIds(object)
, pubMedIds(eSet,value)
experimentData
.abstract(object)
:experimentData
.annotation(object)
,
annotation(object) <- value
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
:featureNames
Standard generic methods:
initialize(object)
:validObject(object)
:phenoData
rows match the number and names of
assayData
columnsshow(object)
dim(object)
, ncol
dim
) or column numbers (ncol
), of all
memebers (dims
) of assayData
.object[(index)
:object
, eSet$<-
phenoData
Additional functions:
updateOldESet
eSet
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
.
# create an instance of an existing derived class new("ExpressionSet") # update existing exprSet-like class to existing derived class data(sample.exprSet) expressionSet <- as(sample.exprSet,"ExpressionSet") expressionSet # 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"))