| GeneIdentifierType {GSEABase} | R Documentation |
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()).
NullIdentifier(annotation, ...) EnzymeIdentifier(annotation, ...) ENSEMBLIdentifier(annotation, ...) GenenameIdentifier(annotation,...) RefseqIdentifier(annotation,...) SymbolIdentifier(annotation,...) UnigeneIdentifier(annotation,...) EntrezIdentifier(annotation,...) AnnotationIdentifier(annotation, ...)
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. |
An object of the same class as the function name, initialized as appropriate for the identifier.
Martin Morgan <mtmorgan@fhcrc.org>
GeneIdentifierType-class for a description of the
classes and methods using these objects.
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")