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.
Usage
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
#> # ℹ 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
#> # ℹ 27 more rows