Looked up by rsID, which is what gnomAD's variant query takes.
Arguments
- rsid
A dbSNP rsID.
- dataset
The gnomAD dataset.
- ...
Passed to
biohttp::post_json().
Value
A biohttp envelope whose data is the list described in
gnomad_parse_frequency().
An rsID does not identify an allele
7:g.140753336A>T and 7:g.140753336A>C both map to rs113488022. Any
lookup routed through an rsID is therefore lossy, and it fails silently
while looking entirely plausible. The canonical key is
(assembly, chromosome, position, ref, alt).
This function is faithful to what gnomAD's variant query accepts, so the limitation is gnomAD's rather than this package's. Know about it before you rely on the answer for a multi-allelic site.
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
# \donttest{
biohttp::body_or_null(gnomad_frequency("rs113488022"))
#> $variant_id
#> [1] "7-140753336-A-T"
#>
#> $dataset
#> [1] "gnomad_r4"
#>
#> $exome
#> $exome$af
#> [1] 1.369283e-06
#>
#> $exome$ac
#> [1] 2
#>
#> $exome$an
#> [1] 1460618
#>
#>
#> $genome
#> NULL
#>
#> $populations
#> # A tibble: 9 × 5
#> pop label ac an af
#> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 sas South Asian 1 86244 0.0000116
#> 2 nfe European (non-Finnish) 1 1111098 0.000000900
#> 3 remaining Remaining 0 60330 0
#> 4 amr Admixed American 0 44684 0
#> 5 fin European (Finnish) 0 53382 0
#> 6 mid Middle Eastern 0 5746 0
#> 7 asj Ashkenazi Jewish 0 26098 0
#> 8 eas East Asian 0 39610 0
#> 9 afr African / African-American 0 33426 0
#>
# }