eSet
Class to Contain High-Throughput Assays and Experimental Metadata
Container for high-throughput assays and experimental
metadata. Classes derived from 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.
- Keywords
- classes
Creating Objects
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
.
Slots
Introduced in eSet
:
assayData
:- Contains matrices with equal
dimensions, and with column number equal to
nrow(phenoData)
. Class:AssayData-class
phenoData
:- Contains experimenter-supplied variables
describing sample (i.e., columns in
assayData
) phenotypes. Class:AnnotatedDataFrame-class
featureData
:- Contains variables describing features
(i.e., rows in
assayData
) unique to this experiment. Use theannotation
slot to efficiently reference feature data common to the annotation package used in the experiment. Class:AnnotatedDataFrame-class
experimentData
:- Contains details of experimental
methods. Class:
MIAME-class
annotation
:- Label associated with the annotation
package used in the experiment. Class:
character
protocolData
:- Contains microarray equipment-generated
variables describing sample (i.e., columns in
assayData
) phenotypes. Class:AnnotatedDataFrame-class
.__classVersion__
:- A
Versions
object describing the R and Biobase version numbers used to created the instance. Intended for developer use.
Methods
Methods defined in derived classes (e.g., ExpressionSet-class
,
SnpSet-class
) may override the methods described here. Class-specific methods:
sampleNames(object)
andsampleNames(object)<-value
:- Coordinate accessing and setting
sample names in
assayData
andphenoData
featureNames(object)
,featureNames(object) <- value
:- Coordinate accessing and setting of
feature names (e.g, genes, probes) in
assayData
. dimnames(object)
,dimnames(object) <- value
:- Also
rownames
andcolnames
; access and set feature and sample names. dims(object)
:- Access the common dimensions (
dim
) or column numbers (ncol
), or dimensions of all members (dims
) ofassayData
. phenoData(object)
,phenoData(object) <- value
:- Access and set
phenoData
. Adding new columns tophenoData
is often more easily done witheSetObject[["columnName"]] <- value
. pData(object)
,pData(object) <- value
:- Access and set
sample data information. Adding new columns to
pData
is often more easily done witheSetObject[["columnName"]] <- value
. varMetadata(object)
,varMetadata(eSet,value)
- Access and set metadata describing
variables reported in
pData
varLabels(object)
,varLabels(eSet, value)<-
:- Access and set variable labels in
phenoData
. featureData(object)
,featureData(object) <- value
:- Access and set
featureData
. fData(object)
,fData(object) <- value
:- Access and set feature data information.
fvarMetadata(object)
,fvarMetadata(eSet,value)
- Access and set metadata describing
features reported in
fData
fvarLabels(object)
,fvarLabels(eSet, value)<-
:- Access and set variable labels in
featureData
. assayData(object), assayData(object) <- value
:-
signature(object = "eSet", value = "AssayData")
: Access and replace theAssayData
slot of aneSet
instance.assayData
returns a list or environment; elements inassayData
not accessible in other ways (e.g., viaexprs
applied directly to theeSet
) can most reliably be accessed with, e.g.,assayData(obj)[["se.exprs"]]
. experimentData(object)
,experimentData(object) <- value
:- Access and set details of experimental methods
description(object)
,description(object) <- value
:- Synonymous with experimentData.
notes(object)
,notes(object) <- value
:-
signature(object="eSet", value="list")
Retrieve and set unstructured notes associated witheSet
.signature(object="eSet", value="character")
As with value="list", but append value to current list of notes. pubMedIds(object)
,pubMedIds(eSet,value)
- Access
and set PMIDs in
experimentData
. abstract(object)
:- Access abstract in
experimentData
. annotation(object)
,annotation(object) <- value
- Access and set annotation label indicating package used in the experiment.
protocolData(object)
,protocolData(object) <- value
- Access and set the protocol data.
preproc(object)
,preproc(object) <- value
:signature(object="eSet", value="list")
Access and setpreprocessing
information in theMIAME-class
object associated with thiseSet
.combine(eSet,eSet)
:- Combine two
eSet
objects. To be combined, eSets must have identical numbers offeatureNames
, distinctsampleNames
, and identicalannotation
. storageMode(object)
,storageMode(eSet,character)<-
:- Change storage mode
of
assayData
. Can be used to 'unlock' environments, or to change betweenlist
andenvironment
modes of storingassayData
.
initialize(object)
:- Object instantiation, can be called by derived classes but not usually by the user.
validObject(object)
:- Validity-checking method,
ensuring (1) all assayData components have the same number of
features and samples; (2) the number and names of
phenoData
rows match the number and names ofassayData
columns as(eSet, "ExpressionSet")
- Convert instance of class
"eSet"
to instance ofExpressionSet-class
, if possible. as(eSet, "MultiSet")
- Convert instance of class
"eSet"
to instance ofMultiSet-class
, if possible. updateObject(object, ..., verbose=FALSE)
- Update instance to current version, if necessary. Usually called through class inheritance rather than directly by the user. See
updateObject
updateObjectTo(object, template, ..., verbose=FALSE)
- Update instance to current version by updating slots in
template
, if necessary. Usually call by class inheritance, rather than directly by the user. SeeupdateObjectTo
isCurrent(object)
- Determine whether version of object is current. See
isCurrent
isVersioned(object)
- Determine whether object contains a 'version' string describing its structure . See
isVersioned
show(object)
- Informatively display object contents.
dim(object)
,ncol
- Access the common
dimensions (
dim
) or column numbers (ncol
), of all memebers (dims
) ofassayData
. object[(index)
:- Conducts subsetting of matrices and phenoData components
object$name
,object$name<-value
- Access and set
name
column inphenoData
object[[i, ...]]
,object[[i, ...]]<-value
- Access and set column
i
(character or numeric index) inphenoData
. The ... argument can include named variables (especiallylabelDescription
) to be added to varMetadata.
- assayDataElement(object, element)
- Return matrix
element
fromassayData
slot ofobject
. - assayDataElement(object, element) <- value)
- Set element
element
inassayData
slot ofobject
to matrixvalue
- assayDataElementReplace(object, element, value)
- Set element
element
inassayData
slot ofobject
to matrixvalue
- assayDataElementNames(object)
- Return element names in
assayData
slot ofobject
updateOldESet
- Update versions of
eSet
constructued usinglistOrEnv
asassayData
slot (before May, 2006).
See Also
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
.
Examples
# 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")