Man pages for emba
Ensemble Boolean Model Biomarker Analysis
| add_numbers_above_the_bars | Add numbers horizontally above the bars of a barplot |
| assign_link_operator_value_to_equation | Assign link operator value to boolean equation |
| biomarker_mcc_analysis | Biomarker analysis based on MCC model classification |
| biomarker_synergy_analysis | Biomarker analysis per synergy predicted |
| biomarker_tp_analysis | Biomarker analysis based on TP model classification |
| calculate_mcc | Calculate Matthews correlation coefficient vector |
| calculate_models_mcc | Calculate the Matthews correlation coefficient for each model |
| calculate_models_synergies_fn | Count the non-synergies of the observed synergies per model... |
| calculate_models_synergies_fp | Count the predictions of the non-synergistic drug... |
| calculate_models_synergies_tn | Count the non-synergies of the non-synergistic drug... |
| calculate_models_synergies_tp | Count the predictions of the observed synergies per model... |
| construct_network | Construct igraph network graph |
| count_models_that_predict_synergies | Count models that predict a set of synergies |
| emba | emba |
| filter_network | Filter the network's vertices |
| get_alt_drugname | Get alternative drug combination name |
| get_avg_activity_diff_based_on_mcc_clustering | Get the average activity difference based on MCC clustering |
| get_avg_activity_diff_based_on_specific_synergy_prediction | Get average activity difference based on specific synergy... |
| get_avg_activity_diff_based_on_synergy_set_cmp | Get the average activity difference based on the comparison... |
| get_avg_activity_diff_based_on_tp_predictions | Get the average activity difference based on the number of... |
| get_avg_activity_diff_mat_based_on_mcc_clustering | Get average activity difference matrix based on MCC... |
| get_avg_activity_diff_mat_based_on_specific_synergy_prediction | Get average activity difference matrix based on specific... |
| get_avg_activity_diff_mat_based_on_tp_predictions | Get average activity difference matrix based on the number of... |
| get_avg_link_operator_diff_based_on_synergy_set_cmp | Get the average link operator difference based on the... |
| get_avg_link_operator_diff_mat_based_on_mcc_clustering | Get average link operator difference matrix based on MCC... |
| get_avg_link_operator_diff_mat_based_on_specific_synergy_prediction | Get average link operator difference matrix based on specific... |
| get_avg_link_operator_diff_mat_based_on_tp_predictions | Get average link operator difference matrix based on the... |
| get_biomarkers | Get total biomarkers from average data differences matrix |
| get_biomarkers_per_type | Get biomarkers from average data differences matrix (per... |
| get_edges_from_topology_file | Get the edges from a specified topology |
| get_fitness_from_models_dir | Load the models fitness scores |
| get_link_operators_from_models_dir | Load the models boolean equation link operator data |
| get_model_names | Get the model names |
| get_model_predictions | Load the models predictions data |
| get_models_based_on_mcc_class_id | Get models based on the MCC class id |
| get_neighbors | Get neighbor nodes |
| get_node_colors | Get the node colors |
| get_node_names | Get the node names |
| get_observed_model_predictions | Subset the model predictions to the (true) observed synergies |
| get_observed_synergies | Load the observed synergies data |
| get_observed_synergies_per_cell_line | Get observed synergies per cell line |
| get_perf_biomarkers_per_cell_line | Get performance biomarkers per cell line |
| get_stable_state_from_models_dir | Load the models stable state data |
| get_synergy_biomarkers_from_dir | Get synergy biomarkers from dir |
| get_synergy_biomarkers_per_cell_line | Get synergy biomarkers per cell line |
| get_synergy_comparison_sets | Get synergy comparison sets |
| get_synergy_scores | Get synergy scores from file |
| get_synergy_subset_stats | Find the number of predictive models for every synergy subset |
| get_unobserved_model_predictions | Subset the model predictions to the (false) non-observed... |
| get_vector_diff | Calculate difference vector with penalty term |
| get_x_axis_values | Get the refined x-axis values |
| is_comb_element_of | Is drug combination element of given vector? |
| make_barplot_on_models_stats | Bar plot of model stats |
| make_barplot_on_synergy_subset_stats | Bar plot of observed synergy subsets |
| plot_avg_link_operator_diff_graph | Plot the graph of average link operator differences (igraph) |
| plot_avg_link_operator_diff_graphs | Plot the graphs from an average link operator differences... |
| plot_avg_state_diff_graph | Plot the graph of average state differences (igraph) |
| plot_avg_state_diff_graphs | Plot the graphs from an average state differences matrix |
| plot_avg_state_diff_graph_vis | Plot the graph of average state differences (visNetwork) |
| plot_mcc_classes_hist | Plot histogram of the MCC classes |
| print_biomarkers_per_predicted_synergy | Print biomarkers for each predicted synergy |
| print_model_and_drug_stats | Print model and drug statistics |
| update_biomarker_files | Update biomarker files for a specific synergy |
| validate_observed_synergies_data | Validate observed synergies data |
