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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", ..., 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.

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

remart::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"
)
remart::getGene(
  id = ids,
  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 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       17294951     17413528
#> 2              17   NA     -1       44248390     44268162