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-class
phenoData
:assayData
) phenotypes.
Class: AnnotatedDataFrame-class
featureData
: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-class
experimentData
:MIAME-class
annotation
:character
protocolData
: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 phenoData
featureNames(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)
pData
varLabels(object)
, varLabels(eSet,
value)<-
:phenoData
.featureData(object)
,
featureData(object) <- value
:featureData
.fData(object)
, fData(object) <- value
:fvarMetadata(object)
,
fvarMetadata(eSet,value)
fData
fvarLabels(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) <- value
protocolData(object)
,
protocolData(object) <- value
preproc(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)
updateObject
updateObjectTo(object, template, ..., verbose=FALSE)
template
, if necessary. Usually call by class inheritance, rather than directly by the user. See updateObjectTo
isCurrent(object)
isCurrent
isVersioned(object)
isVersioned
show(object)
dim(object)
, ncol
dim
) or column numbers (ncol
), of all
memebers (dims
) of assayData
.object[(index)
:object$name
, object$name<-value
name
column in phenoData
object[[i, ...]]
, object[[i, ...]]<-value
i
(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 value
element
in assayData
slot of object
to matrix value
assayData
slot of object
updateOldESet
eSet
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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