mapIdentifiers-methods: Methods for Function mapIdentifiers in Package `GSEABase'
Description
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).
Methods
The following methods are defined on what="GeneSet":
- what = "ANY", to = "ANY", from = "ANY", verbose=FALSE
-
This method warns of attempts to map
from and to the
same type, or generates an error if no suitable
mapIdentifiers methods are available. - what = "GeneSet", to = "GeneIdentifierType", from = "missing", verbose=FALSE
-
This method will re-dispatch to a method with signature
signature(what=what, to=to, from=geneIdType(what)), and is
present so that a user can call mapIdentifiers without providing an
explicit from argument. - what = "GeneSet", to = "GeneIdentifierType", from = "NullIdentifier", verbose=FALSE
-
This maps a gene set from gene identifiers represented by the
NullIdentifier type (i.e., no type associated with the genes) to
gene identifiers represent by any class derived from
GeneIdentifierType. - what = "GeneSet", to = "NullIdentifier", from = "GeneIdentifierType", verbose=FALSE
-
This maps a gene set from gene identifiers represented by any
GeneIdentifierType type to one represented by the
NullIdentifier (i.e., no type associated with the genes). - what = "GeneSet", to = "GeneIdentifierType", from = "environment", verbose=FALSE
-
Maps identifiers found in
what to the type described by
to, using the map (key-value pairs) found in from. - what = "GeneSet", to = "GeneIdentifierType", from = "AnnDbBimap", verbose=FALSE
-
Maps identifiers found in
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.
- what = "GeneColorSet", to = "GeneIdentifierType", from = "missing", verbose=FALSE
-
This method will re-dispatch to a method with signature
signature(what=what, to=to, from=geneIdType(what)), and is
present so that a user can call mapIdentifiers without providing an
explicit from argument. - what = "GeneColorSet", to = "GeneIdentifierType", from = "NullIdentifier", verbose=FALSE
-
This maps a gene set from gene identifiers represented by the
NullIdentifier type (i.e., no type associated with the genes) to
gene identifiers represent by any class derived from
GeneIdentifierType. - what = "GeneColorSet", to = "NullIdentifier", from = "GeneIdentifierType", verbose=FALSE
-
This maps a gene set from gene identifiers represented by any
GeneIdentifierType type to one represented by the
NullIdentifier (i.e., no type associated with the genes). - what = "GeneColorSet", to = "GeneIdentifierType", from = "environment", verbose=FALSE
-
This method is not implemented, and exists to stop incorrect
application of the
GeneSet method. - what = "GeneColorSet", to = "GeneIdentifierType", from = "AnnDbBimap", verbose=FALSE
-
This method is not implemented, and exists to stop incorrect
application of the
GeneSet method.
A method exists for what="GeneSetCollection":
- what = "GeneSetCollection", to = "GeneIdentifierType", from = "missing", verbose = FALSE
-
Map each gene set in
what to gene identifier type
to, using methods described above.