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,...)
    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 <Martin.Morgan@RoswellPark.org>

### 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

[Package GSEABase version 1.54.0 Index]