get_individuals: Get individuals for a population

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

Get individuals for a population

Description

This function retrieves individual-level information. The data is returned as a tibble where each row is an individual of a given species and the columns are metadata about each individual. See below under section Value for details about each column. Use the function get_populations() to discover the available populations for a species.

Usage

get_individuals(
  species_name = "homo_sapiens",
  population = "1000GENOMES:phase_3:CEU",
  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).
population	Population name. Find the available populations for a given species with get_populations.
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 5 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'.

population

Population.

description

Description of the population.

individual

Individual identifier.

gender

Individual gender.

Ensembl REST API endpoints

get_individuals() makes GET requests to /info/variation/populations/:species:/:population_name.

Examples

# Get human individuals for populaton "1000GENOMES:phase_3:CEU" (default)
get_individuals()

# Get Finnish individuals ("1000GENOMES:phase_3:FIN")
get_individuals(population = '1000GENOMES:phase_3:FIN')

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