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(...) EnzymeIdentifier(...) GenenameIdentifier(...) RefseqIdentifier(...) SymbolIdentifier(...) UnigeneIdentifier(...) EntrezIdentifier(...) AnnotationIdentifier(annotation, ...)
annotation |
(required) A single character string identifying the Bioconductor package from which the annotations are drawn. |
... |
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
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")