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Turn Ensembl transcript consequences into a table

Source: R/ensembl.R
ensembl_parse_consequences.Rd

Pure.

Usage

ensembl_parse_consequences(consequences)

Arguments

consequences

The transcript_consequences array from a VEP record.

Value

A tibble of gene, gene_id, transcript, biotype, consequence, impact, sift, and polyphen. NULL when there are none.

Details

Every consequence is returned, with its biotype, rather than only the protein-coding ones. Which biotypes are worth showing is the caller's call, and a filter here would hide the non-coding rows from a caller that wanted them.

Examples

ensembl_parse_consequences(list(list(
  gene_symbol = "BRAF",
  transcript_id = "ENST00000646891",
  biotype = "protein_coding",
  consequence_terms = list("missense_variant"),
  impact = "MODERATE"
)))
#> # A tibble: 1 × 8
#>   gene  gene_id transcript      biotype        consequence impact sift  polyphen
#>   <chr> <chr>   <chr>           <chr>          <chr>       <chr>  <chr> <chr>   
#> 1 BRAF  NA      ENST00000646891 protein_coding missense_v… MODER… NA    NA