Curated clinical evidence counts for a gene

Usage

civic_gene(symbol, ...)

Arguments

symbol: A HUGO gene symbol.
...: Passed to biohttp::post_json(), for example throttle.

Value

A biohttp envelope whose data is a one-row tibble. See civic_parse_gene().

On the interpolated query

CIViC's gene query takes the symbol as an inline string rather than a GraphQL variable, so the symbol is substituted into the query text. It is run through this package's internal clean_symbol() first, which strips everything outside [A-Za-z0-9._-]. That is what stops a crafted symbol closing the string and appending its own query. Do not remove it, and do not switch to paste0() without it.

References

Griffith et al. (2017). CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer. Nature Genetics 49(2), 170-174. doi:10.1038/ng.3774

Service documentation: https://civicdb.org/

Examples

# \donttest{
biohttp::body_or_null(civic_gene("NF1"))
#> # A tibble: 1 × 7
#>   id    symbol entrez_id evidence_items assertions variants source_url          
#>   <chr> <chr>  <chr>              <dbl>      <dbl>    <dbl> <chr>               
#> 1 3867  NF1    4763                  57          0       38 https://civicdb.org…
# }