# Ensemble Boolean Model Biomarker Analysis

## Documentation for package ‘emba’ version 0.1.8

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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 (FN)
calculate_models_synergies_fp | Count the predictions of the non-synergistic drug combinations per model (FP)
calculate_models_synergies_tn | Count the non-synergies of the non-synergistic drug combinations per model (TN)
calculate_models_synergies_tp | Count the predictions of the observed synergies per model (TP)
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 prediction
get_avg_activity_diff_based_on_synergy_set_cmp | Get the average activity difference based on the comparison of two synergy sets
get_avg_activity_diff_based_on_tp_predictions | Get the average activity difference based on the number of true positives
get_avg_activity_diff_mat_based_on_mcc_clustering | Get average activity difference matrix based on MCC clustering
get_avg_activity_diff_mat_based_on_specific_synergy_prediction | Get average activity difference matrix based on specific synergy prediction
get_avg_activity_diff_mat_based_on_tp_predictions | Get average activity difference matrix based on the number of true positives
get_avg_link_operator_diff_based_on_synergy_set_cmp | Get the average link operator difference based on the comparison of two synergy sets
get_avg_link_operator_diff_mat_based_on_mcc_clustering | Get average link operator difference matrix based on MCC clustering
get_avg_link_operator_diff_mat_based_on_specific_synergy_prediction | Get average link operator difference matrix based on specific synergy prediction
get_avg_link_operator_diff_mat_based_on_tp_predictions | Get average link operator difference matrix based on the number of true positives
get_biomarkers | Get total biomarkers from average data differences matrix
get_biomarkers_per_type | Get biomarkers from average data differences matrix (per type)
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_models_based_on_mcc_class_id | Get models based on the MCC class id
get_model_names | Get the model names
get_model_predictions | Load the models predictions data
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 synergies
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 matrix
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