The goal of gwasOncoX is to offer an R package that simplifies the process of retrieving variant data and track files (VCF, BED) for low-to-moderate risk variants associated with cancer, as found in genome-wide association studies. The package utilizes the googledrive R package to download the pre-processed and documented datasets to a local cache directory provided by the user.
remotes::install_github('sigven/gwasOncoX')
The package offers (currently) three different functions:
-
get_variants()- retrieves phenotype information related to GWAS variants in cancer (and GWAS catalog metadata - version, citation etc.) -
get_bed()- retrieves BED tracks ( grch37 and grch38 ) for variants associated with cancer -
get_vcf()- retrieves VCF files ( grch37 and grch38 ) for variants associated with cancer.
If you use the datasets provided with gwasOncoX, make sure you properly cite the the NHGRI-EBI Catalog of human genome-wide association studies:
sigven AT ifi.uio.no