Turn an aliased gnomAD variant response into a table

Pure. The batched query uses aliases v1, v2, and so on, so rows are mapped back by alias index rather than by the echoed id. A variant gnomAD has not seen comes back as null under its alias, with a "Variant not found" entry in errors, and becomes a row of NA.

Usage

gnomad_parse_variants(body, variant_ids)

Arguments

body

A parsed gnomAD GraphQL response body.

variant_ids

The ids that were queried, in the order asked.

Value

A tibble with one row per entry in variant_ids, same order. See gnomad_parse_variant() for the columns.

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

body <- list(data = list(
  v1 = list(variant_id = "17-7676154-G-C", exome = list(af = 0.72)),
  v2 = NULL
))
gnomad_parse_variants(body, c("17-7676154-G-C", "17-7676154-G-GTTTTT"))
#> # A tibble: 2 × 16
#>   variant_id  rsid  exome_af exome_ac exome_an exome_nhomalt genome_af genome_ac
#>   <chr>       <chr>    <dbl>    <dbl>    <dbl>         <dbl>     <dbl>     <dbl>
#> 1 17-7676154… NA        0.72       NA       NA            NA        NA        NA
#> 2 17-7676154… NA       NA          NA       NA            NA        NA        NA
#> # ℹ 8 more variables: genome_an <dbl>, genome_nhomalt <dbl>, grpmax_af <dbl>,
#> #   grpmax_an <dbl>, grpmax_id <chr>, faf95 <dbl>, faf95_pop <chr>,
#> #   filters <chr>