get_vep_consequence: find the VEP consequence for a variant

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

Description

find the VEP consequence for a variant

Usage

get_vep_consequence(variant, include_hgvs = FALSE,
  include_deleterious_score = FALSE, build = "grch37", verbose = FALSE)

Arguments

variant	data frame or list for a variant, containing columns named "chrom", "start_pos", "end_pos", and "alt_allele" code for a single variant
include_hgvs	whether to also include the HGVS consequence strings for cDNA and protein.
include_deleterious_score	whether to also include SIFT and polyphen predictions
build	genome build to find consequences on
verbose	flag indicating whether to print variants as they are checked

Value

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

Examples

get_vep_consequence(data.frame(chrom=c("1"),
    start_pos=c("1000000"), end_pos=c("1000000"), alt_allele=c("A"),
    ref_allele=c("G")))
get_vep_consequence(list(chrom="1", start_pos="1000000",
    end_pos="1000000", alt_allele="A", ref_allele="G"))

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