mapIdentifiers-methods {GSEABase} | R Documentation

## 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.

[Package GSEABase version 1.54.0 Index]