API for LUCIDus
LUCID with Multiple Omics Data
| Global functions | |
|---|---|
| .append_significance | Source code |
| .default_layer_colors | Source code |
| .detect_lucid_model | Source code |
| .feature_importance | Source code |
| .hard_assign_recursive | Source code |
| .importance_caption | Source code |
| .last_try_error_message | Source code |
| .layer_labels | Source code |
| .lucid_check_and_stabilize_sigma | Source code |
| .lucid_omic_panels | Source code |
| .lucid_safe_log_sum_exp | Source code |
| .lucid_safe_normalize | Source code |
| .lucid_safe_solve | Source code |
| .make_panel | Source code |
| .panel_frame | Source code |
| .panel_var | Source code |
| .perm_all | Source code |
| .profile_bar | Source code |
| .profile_heatmap | Source code |
| .profile_theme | Source code |
| .selectZ_feature_mask | Source code |
| .tint | Source code |
| .value_label | Source code |
| Estep | Source code |
| Estep_early | Source code |
| Estep_early_g | Source code |
| Estep_g | Source code |
| Estep_to_r | Source code |
| Istep_Z | Source code |
| LogSumExp | Source code |
| Mstep_G | Source code |
| Mstep_GtoX | Source code |
| Mstep_XtoY | Source code |
| Mstep_XtoZ | Source code |
| Mstep_Z | Source code |
| `%||%` | Source code |
| align_boot_vector | Source code |
| align_replicate_early | Source code |
| align_replicate_parallel | Source code |
| align_replicate_serial | Source code |
| analyze_missing_pattern | Man page Source code |
| binary | Source code |
| boot_lucid | Man page Source code |
| boot_replicate_status | Source code |
| build_serial_transition_labels_boot | Source code |
| cal_bic_parallel | Source code |
| cal_bic_serial | Source code |
| cal_loglik | Source code |
| cal_loglik_serial | Source code |
| check_K | Source code |
| check_and_stabilize_sigma | Source code |
| check_complete_input | Source code |
| check_convergence | Source code |
| check_imputation_quality | Man page Source code |
| check_na | Man page Source code |
| compute_res_r | Source code |
| covariance_npars | Source code |
| early_gamma_covariate | Source code |
| early_gamma_from_levels | Source code |
| early_gamma_levels | Source code |
| early_npars | Source code |
| early_penalty_value | Source code |
| est_mu | Source code |
| estimate_lucid | Man page Source code |
| extract_early_stage_vector | Source code |
| extract_parallel_boot_vector | Source code |
| extract_parallel_gamma | Source code |
| extract_parallel_stage_vector | Source code |
| extract_serial_boot_template | Source code |
| f.binary.early | Source code |
| f.normal.early | Source code |
| f_GtoX | Source code |
| f_XtoY | Source code |
| f_XtoZ | Source code |
| fill_data | Source code |
| fill_data_lod | Source code |
| fit_early_outcome | Source code |
| fit_parallel_outcome | Source code |
| flatten_serial_Z | Source code |
| gen_ci | Source code |
| gen_cov_matrices | Source code |
| get_cluster_assignment | Man page Source code |
| get_model_rho_values | Source code |
| get_selected_G | Man page Source code |
| get_selected_Z | Man page Source code |
| get_top_omics_features | Man page Source code |
| has_unselected_feature | Source code |
| has_unselected_feature_serial | Source code |
| initialize_Delta | Source code |
| initialize_Mu | Source code |
| initialize_Mu_Sigma | Source code |
| initialize_Sigma | Source code |
| is_binary_family | Source code |
| is_normal_family | Source code |
| lastInd | Source code |
| log_dmvnorm_observed | Source code |
| lse | Source code |
| lse_vec | Source code |
| lucid | Man page Source code |
| lucid_early_par_vector | Source code |
| lucid_par_early | Source code |
| lucid_par_parallel | Source code |
| lucid_par_serial | Source code |
| match_boot_clusters | Source code |
| normal | Source code |
| normalize_bootstrap_model | Source code |
| normalize_family_label | Source code |
| normalize_parallel_beta | Source code |
| normalize_parallel_mu | Source code |
| observed_loglik | Source code |
| omics_order_index | Source code |
| outcome_npars | Source code |
| parallel_delta_coef | Source code |
| parallel_delta_from_coef | Source code |
| parallel_joint_from_marginals | Source code |
| parallel_npars | Source code |
| parallel_state_array | Source code |
| parallel_state_eta | Source code |
| penalized_cluster_block | Source code |
| permute_parallel_array | Source code |
| plot.early_lucid | Man page Source code |
| plot.lucid_parallel | Man page Source code |
| plot.lucid_serial | Man page Source code |
| plot_cluster_omic_profile | Man page Source code |
| pred_lucid | Source code |
| predict_lucid | Man page Source code |
| print.sumlucid_early | Man page Source code |
| print.sumlucid_parallel | Man page Source code |
| print.sumlucid_serial | Man page Source code |
| refit_bootstrap_zero_penalty | Source code |
| relabel_early_parameters | Source code |
| relabel_parallel_parameters | Source code |
| restore_serial_Z_from_data | Source code |
| safe_impute | Man page Source code |
| safe_log | Source code |
| safe_log_sum_exp | Source code |
| safe_normalize | Source code |
| safe_solve | Source code |
| serial_em_control | Source code |
| sim_data | Man page |
| simulated_HELIX_data | Man page |
| split_serial_boot_ci | Source code |
| summarize_missing_stats | Source code |
| summary.early_lucid | Man page Source code |
| summary.lucid_parallel | Man page Source code |
| summary.lucid_serial | Man page Source code |
| summary_lucid | Man page Source code |
| summary_lucid_auxi | Source code |
| summary_lucid_simple | Source code |
| to_parallel_family | Source code |
| tune_lucid | Man page |
| vec_to_array | Source code |
