Map input to human gene orthologs

Map input to human gene orthologs

Usage

mapHumanOrthologs(genes, organism = NULL, ensemblRelease = NULL)

Arguments

genes

character. Gene identifiers.

organism

character(1). Full Latin organism name (e.g. "Homo sapiens").

ensemblRelease

integer(1). Ensembl release version (e.g. 100). We recommend setting this value if possible, for improved reproducibility. When left unset, the latest release available via AnnotationHub/ensembldb is used. Note that the latest version available can vary, depending on the versions of AnnotationHub and ensembldb in use.

Value

DFrame. Data frame containing mapping columns:

• geneId

• geneName

• humanGeneId

• humanGeneName

Details

Genes with identifier versions (e.g. "ENSMUSG00000000001.5") are not currently supported.

Note

Updated 2023-11-28.

See also

• biomaRt::listEnsemblArchives().

• biomaRt::listMarts().

• biomaRt::useMart().

Examples

## Expecting ENSMUSG00000000001, ENSMUSG00000000003 to not match here.
genes <- c(
    "ENSMUSG00000000001", "ENSMUSG00000000003",
    "ENSMUSG00000000028", "ENSMUSG00000000031",
    "ENSMUSG00000000037", "ENSMUSG00000000049"
)
## Protect against Ensembl timeouts causing build checks to fail.
if (goalie::isAnExistingUrl("https://ensembl.org")) {
    try({
        x <- mapHumanOrthologs(genes = genes, ensemblRelease = 87L)
        print(x)
    })
}
#> Error in stop(simpleError(message = msg, call = if (p <- sys.parent(1L)) { : 
#>   Unsupported release.