get_species: Get Ensembl species

Description Usage Arguments Value

View source: R/species.R

Description

This function retrieves species-level information. The data is returned as a tibble where each row is a species and the columns are metadata about each species. See below under section Value for details about each column.

Usage

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get_species(division = get_divisions(), verbose = FALSE,
  warnings = TRUE, progress_bar = TRUE)

Arguments

division

Ensembl division, e.g., "EnsemblVertebrates" or "EnsemblBacteria", or a combination of several divisions. Check function get_divisions to get available Ensembl divisions.

verbose

Whether to be verbose about the http requests and respective responses' status.

warnings

Whether to show warnings.

progress_bar

Whether to show a progress bar.

Value

A tibble of 12 variables:

division

Ensembl division: "EnsemblVertebrates", "EnsemblMetazoa", "EnsemblPlants", "EnsemblProtists", "EnsemblFungi" or "EnsemblBacteria".

taxon_id

NCBI taxon identifier.

species_name

Ensembl species name: this is the name used internally by Ensembl to uniquely identify a species by name. It is the scientific name but formatted without capitalisation and spacing converted with an underscore, e.g., 'homo_sapiens'.

species_display_name

Species display name: the name used for display on Ensembl website.

species_common_name

Species common name.

release

Ensembl release version.

genome_assembly_name

Code name of the genome assembly.

genbank_assembly_accession

Genbank assembly accession identifier.

strain

Species strain.

strain_collection

Species strain collection.

species_aliases

Other names or acronyms used to refer to the species. Note that this column is of the list type.

groups

Ensembl databases for which data exists for this species. Note that this column is of the list type.


ramiromagno/ensemblr documentation built on Nov. 5, 2019, 2:59 a.m.