Turn an aliased gnomAD constraint response into a table

Pure. The batched query uses GraphQL aliases g1, g2, and so on, so the response is keyed by alias rather than by symbol. Rows are mapped back by alias index rather than by the echoed symbol, so the result stays aligned even for a gene gnomAD does not return a symbol for.

Usage

gnomad_parse_constraints(body, symbols)

Arguments

body

A parsed gnomAD GraphQL response body.

symbols

The gene symbols that were queried, in the order asked.

Value

A tibble with one row per entry in symbols, same order. A gene with no constraint block gets a row of NA rather than being dropped.

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(
  g1 = list(symbol = "BRAF", gnomad_constraint = list(oe_lof_upper = 0.23)),
  g2 = list(symbol = "TP53", gnomad_constraint = NULL)
))
gnomad_parse_constraints(body, c("BRAF", "TP53"))
#> # A tibble: 2 × 8
#>   symbol   pli loeuf oe_lof oe_mis mis_z syn_z lof_z
#>   <chr>  <dbl> <dbl>  <dbl>  <dbl> <dbl> <dbl> <dbl>
#> 1 BRAF      NA  0.23     NA     NA    NA    NA    NA
#> 2 TP53      NA NA        NA     NA    NA    NA    NA