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

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 argument to from.
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 = "GeneIdentifierType", from = "AnnotationIdentifier", verbose=FALSE
Maps between identifiers of type 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="").
what = "GeneSet", to = "GeneIdentifierType", from = "environment", verbose=FALSE
Maps between identifiers found in from to those in to, using the map (key-value pairs) found in with.
what = "GeneSet", to = "AnnotationIdentifier", 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 = "AnnotationIdentifier", from = "GeneIdentifierType", verbose=FALSE
Maps between identifiers of type 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 = "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 1.0.3 Index]