Get individuals for a population

Source: R/individuals.R

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.

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()

#> # A tibble: 99 × 5
#>    species_name population              description          individual   gender
#>    <chr>        <chr>                   <chr>                <chr>        <chr> 
#>  1 homo_sapiens 1000GENOMES:phase_3:CEU Utah residents with… 1000GENOMES… Female
#>  2 homo_sapiens 1000GENOMES:phase_3:CEU Utah residents with… 1000GENOMES… Male  
#>  3 homo_sapiens 1000GENOMES:phase_3:CEU Utah residents with… 1000GENOMES… Female
#>  4 homo_sapiens 1000GENOMES:phase_3:CEU Utah residents with… 1000GENOMES… Male  
#>  5 homo_sapiens 1000GENOMES:phase_3:CEU Utah residents with… 1000GENOMES… Female
#>  6 homo_sapiens 1000GENOMES:phase_3:CEU Utah residents with… 1000GENOMES… Male  
#>  7 homo_sapiens 1000GENOMES:phase_3:CEU Utah residents with… 1000GENOMES… Female
#>  8 homo_sapiens 1000GENOMES:phase_3:CEU Utah residents with… 1000GENOMES… Male  
#>  9 homo_sapiens 1000GENOMES:phase_3:CEU Utah residents with… 1000GENOMES… Female
#> 10 homo_sapiens 1000GENOMES:phase_3:CEU Utah residents with… 1000GENOMES… Male  
#> # … with 89 more rows

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

#> # A tibble: 99 × 5
#>    species_name population              description        individual     gender
#>    <chr>        <chr>                   <chr>              <chr>          <chr> 
#>  1 homo_sapiens 1000GENOMES:phase_3:FIN Finnish in Finland 1000GENOMES:p… Female
#>  2 homo_sapiens 1000GENOMES:phase_3:FIN Finnish in Finland 1000GENOMES:p… Female
#>  3 homo_sapiens 1000GENOMES:phase_3:FIN Finnish in Finland 1000GENOMES:p… Male  
#>  4 homo_sapiens 1000GENOMES:phase_3:FIN Finnish in Finland 1000GENOMES:p… Female
#>  5 homo_sapiens 1000GENOMES:phase_3:FIN Finnish in Finland 1000GENOMES:p… Female
#>  6 homo_sapiens 1000GENOMES:phase_3:FIN Finnish in Finland 1000GENOMES:p… Female
#>  7 homo_sapiens 1000GENOMES:phase_3:FIN Finnish in Finland 1000GENOMES:p… Female
#>  8 homo_sapiens 1000GENOMES:phase_3:FIN Finnish in Finland 1000GENOMES:p… Female
#>  9 homo_sapiens 1000GENOMES:phase_3:FIN Finnish in Finland 1000GENOMES:p… Male  
#> 10 homo_sapiens 1000GENOMES:phase_3:FIN Finnish in Finland 1000GENOMES:p… Female
#> # … with 89 more rows