Consequence predictions for many variants

Usage

vep_variants(chrom, pos, ref, alt, options = vep_default_options(), ...)

Arguments

chrom, pos, ref, alt: Variant components, all the same length.
options: A named list of VEP request flags. See vep_default_options() for the supported flags and what each one adds to the result.
...: Passed to biohttp::post_json(), for example throttle.

Value

A biohttp envelope whose data is a tibble with one row per variant, in the order asked. See vep_parse_batch().

References

McLaren et al. (2016). The Ensembl Variant Effect Predictor. Genome Biology 17, 122. doi:10.1186/s13059-016-0974-4

Service documentation: https://rest.ensembl.org/

Examples

# \donttest{
biohttp::body_or_null(vep_variants("7", 140753336, "A", "T"))
#> NULL
biohttp::body_or_null(vep_variants(
  "7", 140753336, "A", "T",
  options = c(vep_default_options(), list(af_gnomadg = 1, CADD = 1))
))
#> # A tibble: 1 × 34
#>   key            gene  consequence mane  impact exon  protein_pos sift  polyphen
#>   <chr>          <chr> <chr>       <chr> <chr>  <chr>       <int> <chr> <chr>   
#> 1 7-140753336-A… BRAF  missense_v… NM_0… MODER… 15/18         600 dele… probabl…
#> # ℹ 25 more variables: alphamissense <dbl>, alphamissense_class <chr>,
#> #   transcript <chr>, gene_id <chr>, biotype <chr>, hgvsc <chr>, hgvsp <chr>,
#> #   canonical <lgl>, codons <chr>, amino_acids <chr>, cadd_phred <dbl>,
#> #   cadd_raw <dbl>, revel <dbl>, spliceai_ds_ag <dbl>, spliceai_ds_al <dbl>,
#> #   spliceai_ds_dg <dbl>, spliceai_ds_dl <dbl>, spliceai_max <dbl>, lof <chr>,
#> #   rsid <chr>, gnomadg_af <dbl>, gnomade_af <dbl>, gnomadg_af_max <dbl>,
#> #   gnomade_af_max <dbl>, clin_sig <chr>
# }