Gene constraint for many genes

Batched through GraphQL aliases, so a gene list costs a handful of requests rather than one per gene. Chunked at chunk_size to stay under gnomAD's query cost cap of 25. See GNOMAD_CHUNK.

Usage

gnomad_constraints(
  symbols,
  reference_genome = "GRCh38",
  chunk_size = GNOMAD_CHUNK,
  ...
)

Arguments

symbols

Gene symbols.

reference_genome

"GRCh38" or "GRCh37".

chunk_size

Genes per request.

...

Passed to biohttp::post_json(), for example throttle.

Value

A biohttp envelope whose data is a tibble with one row per entry in symbols, in the same order.

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_constraints(c("BRAF", "TP53", "EGFR")))
#> # A tibble: 3 × 8
#>   symbol   pli loeuf oe_lof oe_mis mis_z  syn_z lof_z
#>   <chr>  <dbl> <dbl>  <dbl>  <dbl> <dbl>  <dbl> <dbl>
#> 1 BRAF   1.000 0.232  0.153  0.577  5.52  1.02   7.35
#> 2 TP53   1.000 0.418  0.258  0.885  1.12  0.651  4.29
#> 3 EGFR   0.389 0.505  0.406  0.828  2.92 -0.454  6.03
# }