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Retries gene annotation information from Ensembl.

Source: R/getGene.R
getGene.Rd

Retries gene annotation information from Ensembl.

Usage

getGene(id, type = "ensembl_gene_id", ..., version = NULL, species = NULL)

Arguments

id

vector of gene identifiers one wants to annotate

type

type of identifier, possible values can be obtained by the listFilters function. Examples are entrezgene_id, hgnc_symbol (for hugo gene symbol), ensembl_gene_id, unigene, agilentprobe, affy_hg_u133_plus_2, refseq_dna, etc.

...

Ignored. Used to catch no longer necessary parameters such as mart from biomaRt functions.

version

Ensembl version to use for the query. If NULL, the latest version will be used.

species

Ensembl name (e.g. "mouse" or "mus_musculus") of the species to look Ensembl IDs for if, e.g., external_gene_name is provided in filters. In biomaRt, this was inferred from the mart argument, but since this argument is no longer used, the species must be provided explicitly.

Value

A data frame containing the following gene annotations for the requested IDs:

  • ensembl_gene_id

  • hgnc_symbol

  • description

  • chromosome_name

  • band (not available from Ensembl REST API, will be filled with NA)

  • strand

  • start_position

  • end_position

Examples

# \donttest{
getGene(
  "ENSG00000157764",
  type = "ensembl_gene_id"
)
#> Warning: 'band' column information is not available from the Ensembl REST API, it will be filled with NA values.
#>   ensembl_gene_id hgnc_symbol
#> 1 ENSG00000157764        BRAF
#>                                                                        description
#> 1 B-Raf proto-oncogene, serine/threonine kinase [Source:HGNC Symbol;Acc:HGNC:1097]
#>   chromosome_name band strand start_position end_position
#> 1               7   NA     -1      140719327    140925199

ids <- c(
 "ENSG00000003987",
 "ENSG00000004939"
)
getGene(
  id = ids,
  type = "ensembl_gene_id",
  version = "may2025"
)
#> Warning: 'band' column information is not available from the Ensembl REST API, it will be filled with NA values.
#>   ensembl_gene_id hgnc_symbol
#> 1 ENSG00000003987       MTMR7
#> 2 ENSG00000004939      SLC4A1
#>                                                                                description
#> 1                        myotubularin related protein 7 [Source:HGNC Symbol;Acc:HGNC:7454]
#> 2 solute carrier family 4 member 1 (Diego blood group) [Source:HGNC Symbol;Acc:HGNC:11027]
#>   chromosome_name band strand start_position end_position
#> 1               8   NA     -1       17296794     17413528
#> 2              17   NA     -1       44248390     44268141
# }