Turn a ClinVar esummary record into a table — clinvar_parse

Pure. Takes one record from the result block of an esummary response, not the whole response, because the record is keyed by UID and the caller already knows which UID it asked for.

Usage

clinvar_parse_record(record, uid = NA_character_)

Arguments

record: A parsed ClinVar esummary record.
uid: The ClinVar UID the record came from.

Value

A one-row tibble with uid, accession, title, significance, review_status, last_evaluated, and conditions. NULL when record is absent.

References

Landrum et al. (2018). ClinVar: improving access to variant interpretations and supporting evidence. Nucleic Acids Research 46(D1), D1062-D1067. doi:10.1093/nar/gkx1153

Service documentation: https://www.ncbi.nlm.nih.gov/clinvar/

Examples

record <- list(
  accession = "VCV000040389",
  title = "NM_004333.6(BRAF):c.1799T>G (p.Val600Gly)",
  germline_classification = list(
    description = "Pathogenic",
    review_status = "reviewed by expert panel"
  )
)
clinvar_parse_record(record, "40389")
#> # A tibble: 1 × 7
#>   uid   accession    title  significance review_status last_evaluated conditions
#>   <chr> <chr>        <chr>  <chr>        <chr>         <chr>          <chr>     
#> 1 40389 VCV000040389 NM_00… Pathogenic   reviewed by … NA             NA