Workflow for running an elastic net model on summary statistics
This workflow implements the elastic net model from the prsmixsumstats R package.
| input | description |
|---|---|
| sumstats | RDS file with summary statistics |
| trait_type | "binary" or "quant" |
| maxiter | (optional) maximum number of iterations to attempt for each (alpha,lambda), default 500 |
| output | description |
|---|---|
| glmnet_fit | RDS file with grid of fits for a range of alpha and lambda |
| glmnet_metrics | metrics corresponding to each element of glmnet_fit: AUC, loss, nbeta (count where abs(beta) > 1e-6) |
| best_model | RDS file with list of two models: min_loss and min_bic |
| mean_loss_plot | plot showing mean loss for each model in the grid, with best models highlighted |