GeneIdentifierType {GSEABase}R Documentation

Gene Identifier Class Constructors

Description

Gene identifier classes and functions are used to indicate what the list of genes in a gene set represents (e.g., Entrez gene identifiers are tagged with EntrezIdentifier(), Bioconductor annotations with AnnotationIdentifier()).

Usage

NullIdentifier(annotation, ...)
EnzymeIdentifier(annotation, ...)
ENSEMBLIdentifier(annotation, ...)
GenenameIdentifier(annotation,...)
RefseqIdentifier(annotation,...)
SymbolIdentifier(annotation,...)
UnigeneIdentifier(annotation,...)
EntrezIdentifier(annotation,...)
AnnotationIdentifier(annotation, ...)

Arguments

annotation An optional character string identifying the Bioconductor package from which the annotations are drawn, e.g., ‘hgu95av2’, ‘org.Hs.eg.db’.
... Additional arguments, usually none.

Value

An object of the same class as the function name, initialized as appropriate for the identifier.

Author(s)

Martin Morgan <mtmorgan@fhcrc.org>

See Also

GeneIdentifierType for a description of the classes and methods using these objects.

Examples

NullIdentifier()

data(sample.ExpressionSet)
gs1 <- GeneSet(sample.ExpressionSet[100:109],
               setName="sample1", setIdentifier="100")
geneIdType(gs1) # AnnotationIdentifier

geneIds <- featureNames(sample.ExpressionSet)[100:109]
gs2 <- GeneSet(geneIds=geneIds,
               setName="sample1", setIdentifier="101")
geneIdType(gs2) # NullIdentifier, since no info about genes provided

## Convert...
ai <- AnnotationIdentifier(annotation(sample.ExpressionSet))
geneIdType(gs2) <- ai
geneIdType(gs2)
## ...or provide more explicit construction
gs3 <- GeneSet(geneIds=geneIds, type=ai,
               setName="sample1", setIdentifier="102")

[Package GSEABase version 1.4.0 Index]