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]