├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── R ├── CI.Rsq.R ├── coxgrad.R ├── eval.R ├── fileIO.R ├── functions.R ├── helpers.R ├── old.functions.R ├── plot.R ├── refitting.R └── snpnet.R ├── README.md ├── docker ├── Dockerfile └── README.md ├── helpers ├── export_betas.R ├── export_intermediate_results.sh ├── snpnet_misc.R ├── snpnet_misc.sh ├── snpnet_wrapper.R └── snpnet_wrapper.sh ├── inst └── extdata │ ├── README.md │ ├── sample.pgen │ ├── sample.phe │ ├── sample.psam │ ├── sample.pvar.zst │ └── vars.rds ├── man ├── FID_IID_from_rownames.Rd ├── FID_IID_to_rownames.Rd ├── cat_or_zcat.Rd ├── compose_regression_formula_str.Rd ├── compute_matrix_product.Rd ├── config_params_data_type.Rd ├── count_n_per_split.Rd ├── eval_AUC_CI.Rd ├── eval_CI.Rd ├── eval_r2_CI.Rd ├── fit_glm.Rd ├── fit_glm_across_splits.Rd ├── fit_to_df.Rd ├── get_ID_ALTs.Rd ├── glm_fit_to_r2.Rd ├── parse_covariates.Rd ├── plot_PRS_binomial.Rd ├── plot_PRS_vs_phe.Rd ├── predict_snpnet.Rd ├── 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