| 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")