get_exac_variants_for_gene: get and parse ExAC variants within a gene

In jeremymcrae/recessiveStats: Enrichment of recessive variants within genes

Description

get and parse ExAC variants within a gene

Usage

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 19, 2019, 5:08 a.m.