GeneIdentifierType-class {GSEABase} | R Documentation

## 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.

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.

### Author(s)

Martin Morgan <Martin.Morgan@RoswellPark.org>

### 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")

[Package GSEABase version 1.54.0 Index]