Combine gnomAD per-ancestry counts into one frequency table

Pure. Sums the exome and genome sample sets per ancestry group.

Usage

gnomad_parse_populations(exome_pops, genome_pops)

Arguments

exome_pops, genome_pops

The populations lists from each sample set.

Value

A tibble of pop, label, ac, an, af, sorted by frequency descending. NULL when there is nothing to report.

Details

Sex-split ids such as nfe_XX and the bare XX/XY breakdowns are dropped, by keeping only the known ancestry codes, so the result is one row per ancestry rather than a mix of ancestries and sexes.

References

Chen et al. (2024). A genomic mutational constraint map using variation in 76,156 human genomes. Nature 625(7993), 92-100. doi:10.1038/s41586-023-06045-0

Service documentation: https://gnomad.broadinstitute.org/

Examples

gnomad_parse_populations(
  list(list(id = "nfe", ac = 3, an = 1000)),
  list(list(id = "nfe", ac = 1, an = 500))
)
#> # A tibble: 1 × 5
#>   pop   label                     ac    an      af
#>   <chr> <chr>                  <dbl> <dbl>   <dbl>
#> 1 nfe   European (non-Finnish)     4  1500 0.00267