Turn one MyVariant record into a table row

Pure.

Usage

myvariant_parse_record(record)

Arguments

record

A parsed MyVariant record.

Value

A one-row tibble of gene, revel, cadd, clinpred, alphamissense, and clinvar_sig.

CADD's key is not what you would guess

Every other dbNSFP predictor exposes <name>.rankscore. CADD does not: it is cadd.raw_rankscore, and there is no plain cadd.rankscore. Following the pattern gives NA for CADD on every variant with nothing to indicate it.

References

Xin et al. (2016). High-performance web services for querying gene and variant annotation. Genome Biology 17, 91. doi:10.1186/s13059-016-0953-9

Service documentation: https://myvariant.info/

Examples

record <- list(dbnsfp = list(
  genename = list("TP53"),
  cadd = list(raw_rankscore = 0.17018),
  revel = list(rankscore = 0.4)
))
myvariant_parse_record(record)
#> # A tibble: 1 × 6
#>   gene  revel  cadd clinpred alphamissense clinvar_sig
#>   <chr> <dbl> <dbl>    <dbl>         <dbl> <chr>      
#> 1 TP53    0.4 0.170       NA            NA NA