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()
#> # 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 N… 1000GENOM… Female
#> 2 homo_sapiens 1000GENOMES:phase_3:CEU Utah residents with N… 1000GENOM… Male
#> 3 homo_sapiens 1000GENOMES:phase_3:CEU Utah residents with N… 1000GENOM… Female
#> 4 homo_sapiens 1000GENOMES:phase_3:CEU Utah residents with N… 1000GENOM… Male
#> 5 homo_sapiens 1000GENOMES:phase_3:CEU Utah residents with N… 1000GENOM… Female
#> 6 homo_sapiens 1000GENOMES:phase_3:CEU Utah residents with N… 1000GENOM… Male
#> 7 homo_sapiens 1000GENOMES:phase_3:CEU Utah residents with N… 1000GENOM… Female
#> 8 homo_sapiens 1000GENOMES:phase_3:CEU Utah residents with N… 1000GENOM… Male
#> 9 homo_sapiens 1000GENOMES:phase_3:CEU Utah residents with N… 1000GENOM… Female
#> 10 homo_sapiens 1000GENOMES:phase_3:CEU Utah residents with N… 1000GENOM… Male
#> # ℹ 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
#> # ℹ 89 more rows