Pure. A variant hits many transcripts and only one row can be reported.
Usage
vep_pick_transcript(element)
Arguments
- element
One parsed VEP result element.
Value
One transcript consequence, or NULL when there are none.
Details
The order is MANE Select first, because that is the community's designated
representative transcript; then whichever transcript carries the variant's
most severe consequence; then the first VEP listed. Taking the first outright
reports an arbitrary transcript, often a non-coding one, which makes the
consequence look milder than it is.
Examples
element <- list(
most_severe_consequence = "missense_variant",
transcript_consequences = list(
list(consequence_terms = list("intron_variant")),
list(consequence_terms = list("missense_variant"), mane_select = "NM_1")
)
)
vep_pick_transcript(element)$mane_select
#> [1] "NM_1"
