Downloads and returns a dataset with low to modest risk variants associated
with disease phenotypes - as discovered from genome-wide association studies
(NHGRI-EBI GWAS catalog)
Usage
get_variants(cache_dir = NA, force_overwrite = F, cancer_only = T)
Arguments
- cache_dir
Local directory for data download
- force_overwrite
Logical indicating if local cache should be overwritten
(set to TRUE to re-download if file exists in cache)
- cancer_only
logical indicating retrieval of all variants versus
cancer-associated variants only
Value
a list object with two elements
records - A data frame with variant annotations (phenotype ID,
association p-value, risk allele, PMID etc.) for GWAS Catalog variants
metadata - GWAS Catalog metadata
