Get populations for a species

This function retrieves population-level information. The data is returned as a tibble where each row is a population of a given species and the columns are metadata about each population. See below under section Value for details about each column. The parameter ld_only to restrict populations returned to only populations with linkage disequilibrium information.

get_populations(
  species_name = "homo_sapiens",
  ld_only = TRUE,
  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).
ld_only	Whether to restrict populations returned to only populations with linkage disequilibrium data.
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 4 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.

cohort_size

Cohort sample size.

Ensembl REST API endpoints

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

Examples

# Get all human populations with linkage disequilibrium data
get_populations(species_name = 'homo_sapiens', ld_only = TRUE)
#> # A tibble: 30 × 4
#>    species_name population              description                  cohort_size
#>    <chr>        <chr>                   <chr>                              <int>
#>  1 homo_sapiens 1000GENOMES:phase_3:ACB African Caribbean in Barbad…          96
#>  2 homo_sapiens 1000GENOMES:phase_3:ASW African Ancestry in Southwe…          61
#>  3 homo_sapiens 1000GENOMES:phase_3:BEB Bengali in Bangladesh                 86
#>  4 homo_sapiens 1000GENOMES:phase_3:CDX Chinese Dai in Xishuangbann…          93
#>  5 homo_sapiens 1000GENOMES:phase_3:CEU Utah residents with Norther…          99
#>  6 homo_sapiens 1000GENOMES:phase_3:CHB Han Chinese in Bejing, China         103
#>  7 homo_sapiens 1000GENOMES:phase_3:CHS Southern Han Chinese, China          105
#>  8 homo_sapiens 1000GENOMES:phase_3:CLM Colombian in Medellin, Colo…          94
#>  9 homo_sapiens 1000GENOMES:phase_3:ESN Esan in Nigeria                       99
#> 10 homo_sapiens 1000GENOMES:phase_3:FIN Finnish in Finland                    99
#> # … with 20 more rows

# Get all human populations
get_populations(species_name = 'homo_sapiens', ld_only = FALSE)
#> # A tibble: 37 × 4
#>    species_name population              description                  cohort_size
#>    <chr>        <chr>                   <chr>                              <int>
#>  1 homo_sapiens 1000GENOMES:phase_3:ACB African Caribbean in Barbad…          96
#>  2 homo_sapiens 1000GENOMES:phase_3:AFR African                              661
#>  3 homo_sapiens 1000GENOMES:phase_3:ALL All phase 3 individuals             2504
#>  4 homo_sapiens 1000GENOMES:phase_3:AMR American                             347
#>  5 homo_sapiens 1000GENOMES:phase_3:ASW African Ancestry in Southwe…          61
#>  6 homo_sapiens 1000GENOMES:phase_3:BEB Bengali in Bangladesh                 86
#>  7 homo_sapiens 1000GENOMES:phase_3:CDX Chinese Dai in Xishuangbann…          93
#>  8 homo_sapiens 1000GENOMES:phase_3:CEU Utah residents with Norther…          99
#>  9 homo_sapiens 1000GENOMES:phase_3:CHB Han Chinese in Bejing, China         103
#> 10 homo_sapiens 1000GENOMES:phase_3:CHS Southern Han Chinese, China          105
#> # … with 27 more rows