get_exac_variants_for_gene: get and parse ExAC variants within a gene

Description Usage Arguments Value

View source: R/alleles_exac.R

Description

get and parse ExAC variants within a gene

Usage

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get_exac_variants_for_gene(hgnc, chrom, start = NULL, end = NULL,
  fileName = NULL, check_last_base = FALSE, remove_benign = FALSE)

Arguments

hgnc

HGNC symbol for the gene that we want data for eg "ARID1B"

chrom

chromosome string e.g. "6"

start

start position of region to be investigated (if checking for gene region defined by chromosome coordinates rather than a HGNC-based gene region).

end

end position of region to be investigated (if checking for gene region defined by chromosome coordinates rather than a HGNC-based gene region).

fileName

path to tabis-indexed ExAC VCF file.

check_last_base

boolean for whether to check if last base non-lofs can be LoF.

remove_benign

boolean for whether to exclude missense_variants with polyphen tolerated predictions.

Value

data frame of variants in gene


jeremymcrae/recessiveStats documentation built on May 17, 2017, 6:09 p.m.