EnrichmentBrowser (version 2.2.2)

map.ids: Mapping between gene ID types for feature names of an expression set

Description

Functionality to map feature names of an expression set between common gene ID types such as ENSEMBL and ENTREZ.

Usage

id.types( org )
    map.ids( eset, org=NA, from="ENSEMBL", to="ENTREZID" )

Arguments

eset

Expression set. An object of ExpressionSet-class. Expects the featureNames to be of gene ID type given in argument 'from'.

org

Organism in KEGG three letter code, e.g. ‘hsa’ for ‘Homo sapiens’. See references.

from

Gene ID type from which should be mapped. Corresponds to the gene ID type of the featureNames of argument 'eset'. Defaults to 'ENSEMBL'.

to

Gene ID type to which should be mapped. Corresponds to the gene ID type the featuresNames of argument 'eset' should be updated with. Defaults to 'ENTREZID'.

Value

id.types: character vector listing the available gene ID types for the mapping;map.ids: An object of ExpressionSet.

Details

The function 'id.types' lists the valid values which the arguments 'from' and 'to' can take. This corresponds to the names of the available gene ID types for the mapping.

References

KEGG Organism code http://www.genome.jp/kegg/catalog/org_list.html

See Also

ExpressionSet-class, mapIds, keytypes

Examples

    # create an expression set with 3 genes and 3 samples
    eset <- make.example.data("eset", nfeat=3, nsmpl=3)
    featureNames(eset) <- paste0("ENSG00000000", c("003","005", "419"))
    eset <- map.ids(eset, org="hsa")