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).
The following methods are defined on what="GeneSet"
:
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 from
argument.NullIdentifier
type (i.e., no type associated with the genes) to
gene identifiers represent by any class derived from
GeneIdentifierType
.GeneIdentifierType
type to one represented by the
NullIdentifier
(i.e., no type associated with the genes).what
to the type described by
to
, using the map (key-value pairs) found in from
.what
to the type described by
to
, using the map (key-value pairs) found in from
.
The following methods are defined for what=GeneColorSet
. These methods
map gene- and phenotype color appropriately, and fail if coloring of
gene identifiers involved in several-to-1 mappings conflict.
signature(what=what, to=to, from=geneIdType(what))
, and is
present so that a user can call mapIdentifiers
without providing an
explicit from
argument.NullIdentifier
type (i.e., no type associated with the genes) to
gene identifiers represent by any class derived from
GeneIdentifierType
.GeneIdentifierType
type to one represented by the
NullIdentifier
(i.e., no type associated with the genes).GeneSet
method.GeneSet
method.
A method exists for what="GeneSetCollection"
:
what
to gene identifier type
to
, using methods described above.