GSEABase (version 1.34.0)

GeneIdentifierType-class: Class "GeneIdentifierType"

Description

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.

Objects from the Class

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.

Slots

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.

Methods

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.

See Also

The example below lists GeneIdentifierType classes defined in this package; See the help pages of these classes for specific information.

Examples

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")