fetchClinvar: Fetch missense variants in ClinVar for given gene

In jweile/maveclin: Clinical predictions for MaveDB

Description

Makes a query to the NCBI webservice to fetch the ClinVar entries for the given gene and filters them down to missense variants

Usage

fetchClinvar(gene, stagger = TRUE, overrideCache = FALSE,
  logger = NULL)

Arguments

gene	gene name as in ClinVar (e.g. 'CALM1')
stagger	logical determining whether HTTP requests should be staggered by a third of a second to avoid rejection by the server. Defaults to TRUE.
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

• clinsig The ClinVar clinical significance string (e.g "Likely pathogenic")

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