GeneIdentifierType-class {GSEABase} | R Documentation |
This class provides a way to tag the meaning of gene
symbols in a GeneSet
. For instance, a GeneSet
with gene
names derived from a Bioconductor annotation
package (e.g., via
ExpressionSet
) initially have a
GeneIdentifierType
of AnnotationIdentifier
.
The following classes are available, and derive from tables in ‘annotation’ packages
GeneIdentifierType
.
All GeneIdentifierType
classes have the following slots:
"ScalarCharacter"
containing the character string representation of this
GeneIdentifierType
."ScalarCharacter"
containing the name of the annotation package from which the
identifiers (probe identifiers) are derived.
GeneIdentifierType
classes are used in:
signature(type = "GeneIdentifierType")
:
Create a new GeneSet
using identifiers of
GeneIdentifierType
.signature(type = "GeneIdentifierType")
:
Create a new GeneColorSet
using identifiers of
GeneIdentifierType
.signature(object = "GeneIdentifierType")
:
extract the name of the annotation package as a character string.signature(object = "GeneIdentifierType", value = "character")
:
assign the name of the annotation package as a character string.signature(object = "GeneIdentifierType")
:
return a character string representation of the type of this
object
.signature(object = "GeneSet", verbose=FALSE, value =
"GeneIdentifierType")
: Changes the GeneIdentifierType
of
object
to value
, attempting to convert symbols in
the process. This method calls mapIdentifiers(what=object,
to=value, from=geneIdType(what), verbose=verbose)
.mapIdentifiers
.signature(object = "GeneIdentifierType")
: display
this object.Martin Morgan <mtmorgan@fhcrc.org>
The example below lists GeneIdentifierType
classes defined in
this package; See the help pages of these classes for specific information.
names(getClass("GeneIdentifierType")@subclasses) # create an AnnotationIdentifier, and ask it's type geneIdType(AnnotationIdentifier(annotation="hgu95av2")) # Construct a GeneSet from an ExpressionSet, using the 'annotation' # field of ExpressionSet to recognize the genes as AnnotationType data(sample.ExpressionSet) gs <- GeneSet(sample.ExpressionSet[100:109], setName="sample.GeneSet", setIdentifier="123") geneIdType(gs) # AnnotationIdentifier ## Read a Broad set from the system (or a url), and discover their ## GeneIdentifierType fl <- system.file("extdata", "Broad.xml", package="GSEABase") bsets <- getBroadSets(fl) sapply(bsets, geneIdType) ## try to combine gene sets with different set types try(gs & sets[[1]]) ## Not run: ## Use the annotation package associated with the original ## ExpressionSet to map to EntrezIdentifier() ... geneIdType(gs) <- EntrezIdentifier() ## ...and try again gs & bsets[[1]] ## Another way to change annotation to Entrez (or other) ids probeIds <- featureNames(sample.ExpressionSet)[100:109] geneIds <- getEG(probeIds, "hgu95av2") GeneSet(EntrezIdentifier(), setName="sample.GeneSet2", setIdentifier="101", geneIds=geneIds) ## End(Not run) ## Create a new identifier setClass("FooIdentifier", contains="GeneIdentifierType", prototype=prototype( type=new("ScalarCharacter", "Foo"))) ## Create a constructor (optional) FooIdentifier <- function() new("FooIdentifier") geneIdType(FooIdentifier()) ## tidy up removeClass("FooIdentifier")