Retrieve orthologous gene annotations across two species

Retrieve orthologous gene annotations across two species

Usage

getLDS(
  attributes,
  filters = "",
  values = "",
  attributesL,
  filtersL = "",
  valuesL = "",
  ...,
  species = NULL,
  speciesL = NULL
)

Arguments

attributes

Attributes you want to retrieve of primary dataset. A possible list of attributes can be retrieved using the function listAttributes().

filters

Filters that should be used in the query. These filters will be applied to primary dataset. A possible list of filters can be retrieved using the function listFilters().

values

Values of the filter, e.g. list of affy IDs

attributesL

Attributes of linked dataset that needs to be retrieved

filtersL

Filters to be applied to the linked dataset

valuesL

Values for the linked dataset filters

...

Ignored. Used to catch no longer necessary parameters such as mart, martL, verbose, uniqueRows and bmHeader 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.

speciesL

Ensembl name (e.g. "mouse" or "mus_musculus") of the species to look up orthologues in. This replaces the martL argument used in biomaRt, as connections to Ensembl datasets are no longer needed, but the species of the linked dataset can not be inferred from attributesL/filtersL/valuesL alone.

Value

A data frame containing source-species and target-species ortholog annotations.

Details

This function relies on the Ensembl REST homology/id endpoint, and therefore only supports retrieving orthologues, and not the more general cross-database attribute linking biomaRt::getLDS() could perform.

Supported filters/attributes (for both filters/attributes and filtersL/attributesL): ensembl_gene_id, ensembl_peptide_id, external_gene_name, description, chromosome_name, start_position, end_position, strand, gene_biotype.

Only "ensembl_gene_id" and "external_gene_name" are supported for filter.

Examples

getLDS(
  attributes = c("ensembl_gene_id", "external_gene_name"),
  filters = "ensembl_gene_id",
  values = "ENSG00000157764",
  attributesL = c("ensembl_gene_id", "external_gene_name"),
  speciesL = "mouse"
)
#>   ensembl_gene_id external_gene_name  ensembl_gene_id.1 external_gene_name.1
#> 1 ENSG00000157764               BRAF ENSMUSG00000002413                 Braf

# It is also possible to a gene symbol, but a species must be specified, as
# gene symbols are not unique across species.
getLDS(
  attributes = c("ensembl_gene_id", "external_gene_name"),
  filters = "external_gene_name",
  values = "APOE",
  species = "human",
  attributesL = c("ensembl_gene_id", "external_gene_name"),
  speciesL = "mouse"
)
#>   ensembl_gene_id external_gene_name  ensembl_gene_id.1 external_gene_name.1
#> 1 ENSG00000130203               APOE ENSMUSG00000002985                 Apoe