Retrieve gene/transcript annotations from Ensembl

Usage

getBM(attributes, filters = "", values = "", ..., species = NULL)

Arguments

attributes: Attributes you want to retrieve. A possible list of attributes can be retrieved using the function listAttributes().
filters: Filters (one or more) that should be used in the query. A possible list of filters can be retrieved using the function listFilters().
values: Values of the filter, e.g. vector of affy IDs. If multiple filters are specified then the argument should be a list of vectors of which the position of each vector corresponds to the position of the filters in the filters argument.
...: Ignored. Used to catch no longer necessary parameters such as mart, checkFilters, verbose, uniqueRows, bmHeader, quote and useCache 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 requested gene or transcript annotations, with one column for each requested attribute. The number of rows does not necessarily match the number of requested identifiers, as some attributes can have multiple values for a single identifier (e.g. a gene with multiple transcripts).

Details

Only a subset of the attributes and filters supported by the biomaRt package are currently implemented, as this data has to be retrieved through the Ensembl REST lookup/id endpoint rather than a generic BioMart query engine.

Supported filters (only one can be used at a time): ensembl_gene_id, ensembl_transcript_id, external_gene_name.

Supported attributes: ensembl_gene_id, ensembl_transcript_id, ensembl_peptide_id, external_gene_name, description, chromosome_name, start_position, end_position, strand, gene_biotype, transcript_biotype, version.

Examples

attribs <- c("ensembl_gene_id", "external_gene_name", "chromosome_name")
getBM(
  attributes = attribs,
  filters = "ensembl_gene_id",
  values = c("ENSG00000157764", "ENSG00000004939")
)
#>   ensembl_gene_id external_gene_name chromosome_name
#> 1 ENSG00000157764               BRAF               7
#> 2 ENSG00000004939             SLC4A1              17

# It is also possible to a gene symbol, but a species must be specified, as
# gene symbols are not unique across species.
getBM(
  attributes = attribs,
  filters = "external_gene_name",
  values = c("APOE", "MAPT"),
  species = "human"
)
#>   ensembl_gene_id external_gene_name chromosome_name
#> 1 ENSG00000130203               APOE              19
#> 2 ENSG00000186868               MAPT              17