Bucket a ClinVar significance string into a coarse category

Pure. For colouring and grouping, where the full free-text significance is too granular to plot.

Usage

clinvar_category(significance)

Arguments

significance

A ClinVar clinical significance string.

Value

One of "Conflicting", "Pathogenic / likely", "Benign / likely", "Uncertain", or "Other".

Details

The order of the checks matters. A conflicting record usually contains the word "pathogenic" too, so conflicting has to be tested first or every conflicting record reads as pathogenic.

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

clinvar_category("Pathogenic")
#> [1] "Pathogenic / likely"
clinvar_category("Conflicting interpretations of pathogenicity")
#> [1] "Conflicting"