parse_vep_output: parses VEP output

In jeremymcrae/recessiveStats: Enrichment of recessive variants within genes

Description

parses VEP output

Usage

parse_vep_output(variant, hgnc, remove_benign = TRUE)

Arguments

variant	single row dataframe containing allele column and VEP prediction column.
hgnc	HGNC symbol for the gene that we are currently investigating.
remove_benign	boolean for whether to exclude missense_variants with polyphen tolerated predictions.

Value

vep consequence string for the most severe consequence for the gene of interest. If none of the predicted consequences lie within the gene of interest, return "NA". If the variant has multiple alleles, return a comma-separated list of VEP consequences for the alleles.

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