| adjust_Xnew | adjust Xnew by discarding columns not in Xold_colnames and by... |
| calc_minfo | calculates normalized mutual information given P(variant |... |
| calc_one_v_rest_auc | Calculating area under Precision-Recall curve (PRC) and... |
| create_model | Initialize a fully-connected multi-class neural network |
| divide_rows | Convenience functions for dividing rows and columns of a... |
| extract_cancer_response | Convenience function for extracting cancer (response)... |
| extract_design | Obtain design matrix (X) for variants from a mutation... |
| extract_design_mdesign_mcat | Extract Design-Metadesign (XU) matrix for a categorical... |
| extract_design_mdesign_mcts | Extract Design-Metadesign (XU) matrix for a set of continuous... |
| extract_design_mdesign_sbs96 | Extract Design-Metadesign (XU) matrix for SBS-96 meta-feature... |
| extract_glmnet | Extract the cv.glmnet object from the output of fit_mlogit |
| extract_tmb | #' Extract total mutation burden (TMB) of tumors in a maf... |
| fitness | Fit and validate neural network |
| fit_nnc | Train a fully-connected multi-class neural network |
| fit_rfc | Hidden genome random forest classifier (rfc) |
| fit_smlc | Hidden genome sparse multinomial logistic classifier (smlc) |
| fit_svmc | Hidden genome SVM classifier (svmc) |
| impact | MSK-IMPACT somatic mutation annotation data from 10 common... |
| indiv_predict_effect | Probability distance based effects of predictors in a fitted... |
| new_nn | Generate an object from the class "nn" |
| odds_ratio_mlogit | Calculate odds ratios from a multinomial logistic hidden... |
| optimal_threshold | Determine optimal one-vs-rest classification thresholds from... |
| pipe | Pipe operator |
| predict_nnc | Get neural network predictions |
| predict_rfc | prediction based on hidden genome random forest classifier |
| predict_smlc | Prediction based on the hidden genome sparse multinomial... |
| predict_svmc | prediction based on hidden genome random forest classifier |
| screen_variant_mi | Mutual Information based feature screening of variants from a... |
| tcga | TCGA somatic mutation annotation data from 10 common cancer... |
| tune_model | Tune neural network hyperparameters using Bayesian... |
