| mapIdentifiers-methods {GSEABase} | R Documentation |
These methods convert the genes identifiers of a gene set from one
type to another, e.g., from EntrezIdentifier to
AnnotationIdentifier. Methods can be called directly by
the user; geneIdType<- provides similar
functionality. verbose=TRUE produces warning messages when
maps between identifier types are not 1:1, or a map has to be
constructed on the fly (this situation does not apply when using the
DBI-based annotation packages).
from and to the
same type, or generates an error if no suitable
mapIdentifiers methods are available.signature(what=what, to=to, from=geneIdType(what)), and is
present so that a user can call mapIdentifiers without providing an
explicit argument to from.NullIdentifier type (i.e., no type associated with the genes) to
gene identifiers represent by any class derived from
GeneIdentifierType.AnnotationIdentifier and
other identifiers. This method consults the annotation package specified
in from, looking for a mapping between genes(what) and
paste(annotation(what), toupper(geneIdType(to)), sep="").from to those in
to, using the map (key-value pairs) found in with.NullIdentifier type (i.e., no type associated with the genes) to
gene identifiers represent by any class derived from
GeneIdentifierType.GeneIdentifierType to
AnnotationIdentifier. This method uses the annotation package
specified in from. It tries first to use AnnotationDbi and
DBI-based chip annotations to find the reverse mapping. If that fails,
the method then tries to use the annotation package and
environment-based mappings to find a reverse map.what to gene identifier type
to, using methods described above.