GeneIdentifierType | 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,...) UniprotIdentifier(annotation,...) EntrezIdentifier(annotation,...) AnnotationIdentifier(annotation, ...) AnnoOrEntrezIdentifier(annotation, ...)
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. |
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.
Martin Morgan <Martin.Morgan@RoswellPark.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") uprotIds <- c("Q9Y6Q1", "A6NJZ7", "Q9BXI6", "Q15035", "A1X283", "P55957") gs4 <- GeneSet(uprotIds, geneIdType=UniprotIdentifier()) geneIdType(gs4) # UniprotIdentifier
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