clinvar_gene: Extracting genes from clinvar database NCBI.

In VilainLab/Nanotator: Next generation structural variant annotation and classification

Extracting genes from clinvar database NCBI.

Description

Extracting genes from clinvar database NCBI.

Usage

clinvar_gene(terms, clinvar, downloadClinvar, omimID = NULL)

Arguments

terms	Single or Multiple Terms.
clinvar	character clinvar database location.
downloadClinvar	boolean If TRUE, download the gtr database. Default FALSE.
omimID	numeric Omim Id for disease.

Value

Dataframe returned containing gene lists in entrezid and Gene Symbols, and terms associated with it

Examples

terms="Liver cirrhosis"
clinvar = system.file("extdata", "localPDB/", package="nanotatoR")
downloadClinvar = FALSE
ge <- clinvar_gene(terms = terms, clinvar = clinvar, 
downloadClinvar = downloadClinvar, 
omimID = "OMIM:118980")

VilainLab/Nanotator documentation built on Aug. 2, 2024, 8:45 p.m.