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.