GeneIdentifierType-constructors: Gene Identifier Class Constructors

In GSEABase: Gene set enrichment data structures and methods

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,...)
UniprotIdentifier(annotation,...)
EntrezIdentifier(annotation,...)
AnnotationIdentifier(annotation, ...)
AnnoOrEntrezIdentifier(annotation, ...)

Arguments

annotation	An optional character string identifying the Bioconductor package from which the annotations are drawn, e.g., ‘hgu95av2’, ‘org.Hs.eg.db’. Or an ‘src_organism’ object, e.g. ‘Organism.dplyr::src_organism(TxDb.Hsapiens.UCSC.hg38.knownGene)’.
...	Additional arguments, usually none.

Value

For all but AnnoOrEntrezIdentifier, An object of the same class as the function name, initialized as appropriate for the identifier.

For AnnoOrEntrezIdentifier, either an AnnotationIdentifier or EntrezIdentifier depending on the argument. This requires that the corresponding chip- or organism package be loaded, hence installed on the user's system.

Author(s)

Martin Morgan <[e-mail]>

See Also

GeneIdentifierType-class 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")

uprotIds <- c("Q9Y6Q1", "A6NJZ7", "Q9BXI6", "Q15035", "A1X283",
              "P55957")
gs4 <- GeneSet(uprotIds, geneIdType=UniprotIdentifier())
geneIdType(gs4) # UniprotIdentifier
geneIds(mapIdentifiers(gs4, UnigeneIdentifier(annotation="org.Hs.eg")))

GSEABase documentation built on Dec. 13, 2020, 2 a.m.