idMap {EnrichmentBrowser}R Documentation

Mapping between gene ID types for the rownames of a SummarizedExperiment

Description

Functionality to map the rownames of a SummarizedExperiment between common gene ID types such as ENSEMBL and ENTREZ.

Usage

idMap(se, org = NA, from = "ENSEMBL", to = "ENTREZID")

idTypes(org)

Arguments

se

An object of class SummarizedExperiment. Expects the names 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 names of argument 'se'. Defaults to 'ENSEMBL'.

to

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

Details

The function 'idTypes' 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.

Value

idTypes: character vector listing the available gene ID types for the mapping;

idMap: An object of SummarizedExperiment.

Author(s)

Ludwig Geistlinger <Ludwig.Geistlinger@sph.cuny.edu>

References

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

See Also

SummarizedExperiment, mapIds, keytypes

Examples


    # create an expression dataset with 3 genes and 3 samples
    se <- makeExampleData("SE", nfeat=3, nsmpl=3)
    names(se) <- paste0("ENSG00000000", c("003","005", "419"))
    se <- idMap(se, org="hsa")


[Package EnrichmentBrowser version 2.10.11 Index]