Description Creating Objects Slots Methods Author(s) See Also Examples
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.
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
.
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
the annotation
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 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
:Coordinate accessing and setting
sample names in assayData
and phenoData
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
and colnames
; access and set
feature and sample names.
dims(object)
:Access the common dimensions (dim
) or
column numbers (ncol
), or dimensions of all members
(dims
) of assayData
.
phenoData(object)
,
phenoData(object) <- value
:Access and set
phenoData
. Adding new columns to phenoData
is often
more easily done with eSetObject[["columnName"]] <- value
.
pData(object)
, pData(object) <- value
:Access and set
sample data information. Adding new columns to pData
is often
more easily done with eSetObject[["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 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
: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 with eSet
.
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 set preprocessing
information
in the MIAME-class
object associated with this
eSet
.
combine(eSet,eSet)
:Combine two eSet
objects. To be combined, eSets must have identical numbers of
featureNames
, distinct sampleNames
, and identical annotation
.
storageMode(object)
, storageMode(eSet,character)<-
:Change storage mode
of assayData
. Can be used to 'unlock' environments,
or to change between list
and environment
modes of
storing assayData
.
Standard generic methods:
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 of
assayData
columns
as(eSet, "ExpressionSet")
Convert instance of class "eSet"
to instance of ExpressionSet-class
, if possible.
as(eSet, "MultiSet")
Convert instance of class "eSet"
to instance of MultiSet-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. See updateObjectTo
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
) of assayData
.
object[(index)
:Conducts subsetting of matrices and phenoData components
object$name
, object$name<-value
Access and set name
column in phenoData
object[[i, ...]]
, object[[i, ...]]<-value
Access and set column i
(character or
numeric index) in phenoData
. The ... argument can include
named variables (especially labelDescription
) to be added
to varMetadata.
Additional functions:
Return matrix
element
from assayData
slot of object
.
Set element element
in assayData
slot of
object
to matrix value
. If validate=TRUE
,
check that value row and column names of conform to object.
Set element element
in assayData
slot of object
to matrix value
. If
validate=TRUE
, check that row and column names of value
conform to object.
Return element names in
assayData
slot of object
updateOldESet
Update versions of 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
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | # 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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