get_gwas_variants: Get the variants from the gwas catalog associated to the...

In MCorentin/vargen: Fetching Variants Related to Phenotypes Using Public Databases

Get the variants from the gwas catalog associated to the traits of interest

Description

uses subsetByTraits to get the variants.

Usage

get_gwas_variants(gwas_traits, gwas_cat)

Arguments

gwas_traits	a vector of gwas traits, can be obtained from list_gwas_traits
gwas_cat	output from create_gwas

Value

a data.frame contaning the variants linked to the traits in the gwas catalog The data.frame contains the following columns:

• chr (chromosome)

• pos (position of the variant)

• rsid (variant ID)

• ensembl_gene_id ("gene id" of the gene associated with the variants)

• hgnc_symbol ("hgnc symbol" of the gene associated with the variants)

• source (here "gwas")

Examples

# if you need to get the list of gwas traits:
# list_gwas_traits(keywords = c("Obesity"))
obesity_gwas <- c("Obesity (extreme)", "Obesity-related traits", "Obesity")
gwas_cat <- create_gwas()

gwas_variants <- get_gwas_variants(obesity_gwas, gwas_cat)

MCorentin/vargen documentation built on Feb. 6, 2024, 2:32 p.m.