Genetic-Variant-Prioritization-using-Elastic-Net: Genetic-Variant-Prioritization-using-Elastic-Net

This is the R code for conducting elastic net to produce a prediction value/probability for each genetic variant (SNP) of how likely it is to be a hit/associated SNP from a genome-wide association study (GWAS) given functional genomic annotations. In brief, we propose to combine a Bayes factor for annotation (based on the prediction value from the model) with a Bayes factor for association. For a description of the full method, see: Gagliano SA, Barnes MR, Weale ME, Knight J (2014) A method to incorporate hundreds of functional characteristics with association evidence to improve variant prioritization. PLoS ONE 9: e98122. To access the functional annotations, the prediction values, Bayes factors for annotation (BFannot), and R code to derive Bayes factors for association (BFassoc) see BFannot.BFassoc.zip.