Turn one VEP element into a table row — vep_parse

Pure.

Usage

vep_parse_element(element)

Arguments

element: One parsed VEP result element.

Value

A one-row tibble.

AlphaMissense is nested

It is at transcript_consequences[].alphamissense$am_pathogenicity, per transcript. There is nothing at the top level. Hoisting the read out of the transcript is the single easiest way to get NA everywhere and conclude the API does not serve it.

Examples

element <- list(
  most_severe_consequence = "missense_variant",
  transcript_consequences = list(list(
    gene_symbol = "BRAF", consequence_terms = list("missense_variant"),
    alphamissense = list(am_pathogenicity = 0.99, am_class = "pathogenic")
  ))
)
vep_parse_element(element)
#> # A tibble: 1 × 10
#>   gene  consequence  mane  impact exon  protein_pos sift  polyphen alphamissense
#>   <chr> <chr>        <chr> <chr>  <chr>       <int> <chr> <chr>            <dbl>
#> 1 BRAF  missense_va… NA    NA     NA             NA NA    NA                0.99
#> # ℹ 1 more variable: alphamissense_class <chr>