get_variation_sources: Retrieve variant sources

In ramiromagno/ensemblr: R Client for the Ensembl REST API

Retrieve variant sources

Description

This function retrieves variant sources, i.e. a list of databases used by Ensembl from which variant information is retrieved.

Usage

get_variation_sources(
  species_name = "human",
  verbose = FALSE,
  warnings = TRUE,
  progress_bar = TRUE
)

Arguments

species_name	The species name, i.e., the scientific name, all letters lowercase and space replaced by underscore. Examples: 'homo_sapiens' (human), 'ovis_aries' (Domestic sheep) or 'capra_hircus' (Goat).
verbose	Whether to be chatty.
warnings	Whether to print warnings.
progress_bar	Whether to show a progress bar.

Value

A tibble, each row being a variant database, of 8 variables:

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'.

db_name

Database name.

type

Database type, e.g., chip (genotyping chip) or lsdb (locus-specific database).

version

Database version.

somatic_status

Somatic status.

description

Database description.

url

Database's URL.

data_types

Data types to be found at database.

Ensembl REST API endpoints

get_variation_sources makes GET requests to info/variation/:species.

Examples

# Retrieve variant sources for human (default)
get_variation_sources()

# Retrieve variant sources for mouse
get_variation_sources(species_name = 'mus_musculus')

ramiromagno/ensemblr documentation built on Oct. 19, 2023, 11:12 a.m.