find_most_severe_transcript: find the most severe transcript from Ensembl data

In jeremymcrae/publishedDeNovos: Published De Novos Dataset from Developmental Disorder Sequencing Studies

Description

find the most severe transcript from Ensembl data

Usage

find_most_severe_transcript(ensembl_json, include_hgvs = FALSE,
  exclude_bad = TRUE)

Arguments

ensembl_json	json data for variant from Ensembl
include_hgvs	boolean showing if we will be using HGVS predictions from the VEP consequence predictions. If true, we sort the trasncripts by their length, so that we consistently return the same transcript between different variants from the same gene. Otherwise we just return the first most severe transcript.
exclude_bad	boolean to show whether we want to exclude nonsense mediated decay transcripts and so forth. We only supply a false value for recursive calling, when we have failed to find any transcript during normal usage.

Value

a character string containing the most severe consequence, as per VEP annotation formats.

jeremymcrae/publishedDeNovos documentation built on May 19, 2019, 5:08 a.m.