Turn one Allele Registry element into a table row

Pure.

Usage

clingen_parse_allele(element)

Arguments

element

One parsed Allele Registry element.

Value

A one-row tibble.

An unresolved input is a row, not a gap

ClinGen answers an input it could not resolve with an object carrying no @id, and an errorType/message instead. That becomes a row with resolved = FALSE and the reason, rather than being dropped. Dropping it would shift every later row onto the wrong variant, and would lose the reason the input was rejected.

References

Pawliczek et al. (2018). ClinGen Allele Registry links information about genetic variants. Human Mutation 39(11), 1690-1701. doi:10.1002/humu.23637

Service documentation: https://reg.clinicalgenome.org/

Examples

clingen_parse_allele(list(errorType = "IncorrectHgvsPosition"))
#> # A tibble: 1 × 12
#>   resolved caid  reason             rsid  clinvar_allele_id clinvar_variation_id
#>   <lgl>    <chr> <chr>              <chr>             <int>                <int>
#> 1 FALSE    NA    IncorrectHgvsPosi… NA                   NA                   NA
#> # ℹ 6 more variables: myvariant_hg38 <chr>, chrom <chr>, pos <int>, ref <chr>,
#> #   alt <chr>, title <chr>