fetchGnomad: Fetch missense variants in GnomAD for given gene

In jweile/maveclin: Clinical predictions for MaveDB

Description

Makes a query to the ExAC webservice to fetch the GnomAD entries for the given gene and filters them down to missense variants.

Usage

fetchGnomad(ensemblID, overrideCache = FALSE, logger = NULL)

Arguments

ensemblID	The Ensembl gene identifier (e.g. ENSG00000198668)
overrideCache	logical determining whether local cache should be overridden
logger	a yogilogger object to write log messages to. Defaults to NULL

Value

a data.frame with the following columns:

• hgvsc The HGVS variant descriptor at the coding sequence (DNA) level

• hgvsp The HGVS variant descriptor at the amino acid sequence (Protein) level

• maf The minor allele frequency.

jweile/maveclin documentation built on May 4, 2019, 3:08 a.m.