Turn the colocated variants of a VEP element into a table row

Pure. A VEP element lists the known variants at the same site under colocated_variants: the dbSNP record, and COSMIC and HGMD entries beside it. The dbSNP record is the one carrying population frequencies and clinical significance, so that is the record read. When several dbSNP records are listed, the one with frequencies wins.

Usage

vep_parse_colocated(element)

Arguments

element

One parsed VEP result element.

Value

A one-row tibble of rsid, gnomadg_af, gnomade_af, gnomadg_af_max, gnomade_af_max, and clin_sig, all NA when the element has no dbSNP record.

Details

Frequencies are only present when af, af_gnomade or af_gnomadg was requested, see vep_default_options(). gnomadg_af_max and gnomade_af_max are the largest per-population frequency of that source, which is what a rarity filter wants rather than the overall frequency. clin_sig is the significance of the element's own allele where VEP reports it per allele, so the alleles of a multi-allelic site do not share one answer.

References

McLaren et al. (2016). The Ensembl Variant Effect Predictor. Genome Biology 17, 122. doi:10.1186/s13059-016-0974-4

Service documentation: https://rest.ensembl.org/

Examples

element <- list(
  allele_string = "G/C",
  colocated_variants = list(list(
    id = "rs1042522",
    frequencies = list(C = list(gnomadg = 0.62, gnomadg_afr = 0.38)),
    clin_sig = list("benign")
  ))
)
vep_parse_colocated(element)
#> # A tibble: 1 × 6
#>   rsid      gnomadg_af gnomade_af gnomadg_af_max gnomade_af_max clin_sig
#>   <chr>          <dbl>      <dbl>          <dbl>          <dbl> <chr>   
#> 1 rs1042522       0.62         NA           0.38             NA benign