GeneIdentifierType-class: Class "GeneIdentifierType"
In GSEABase: Gene set enrichment data structures and methods

Description Objects from the Class Slots Methods Author(s) See Also Examples

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

NullIdentifier: No formal information about what gene identifiers represent.
AnnotationIdentifier: Gene identifiers are Affymetrix chip-specific probe identifier, as represented in Bioconductor annotation packages.
EntrezIdentifier: ‘Entrez’ identifiers.
EnzymeIdentifier: ‘EC’ identifiers.
ENSEMBLIdentifier: ‘ENSEMBL’ identifiers.
GenenameIdentifier: Curated and ad hoc descriptive gene names.
RefseqIdentifier: ‘Prosite’ identifiers.
SymbolIdentifier: ‘Symbol’ identifiers.
UnigeneIdentifier: ‘Unigene’ identifiers.
UniprotIdentifier: ‘Uniprot’ identifiers.
GeneIdentifierType: A virtual Class: No objects may be created from it; all classes listed above are subclasses of GeneIdentifierType.

All GeneIdentifierType classes have the following slots:

type: Object of class "ScalarCharacter" containing the character string representation of this GeneIdentifierType.
annotation: Object of class "ScalarCharacter" containing the name of the annotation package from which the identifiers (probe identifiers) are derived.

GeneIdentifierType classes are used in:

GeneSet: signature(type = "GeneIdentifierType"): Create a new GeneSet using identifiers of GeneIdentifierType.
GeneColorSet: signature(type = "GeneIdentifierType"): Create a new GeneColorSet using identifiers of GeneIdentifierType.
annotation: signature(object = "GeneIdentifierType"): extract the name of the annotation package as a character string.
annotation<-: signature(object = "GeneIdentifierType", value = "character"): assign the name of the annotation package as a character string.
geneIdType: signature(object = "GeneIdentifierType"): return a character string representation of the type of this object.
geneIdType<-: 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: See mapIdentifiers.
show: signature(object = "GeneIdentifierType"): display this object.

Martin Morgan <Martin.Morgan@RoswellPark.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")