Function reference • emba

General Run a full biomarker analysis on a given boolean model ensemble dataset
`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
Model Data Differences Get characteristic data model differences based on specified model groupings
`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_vector_diff()`	Calculate difference vector with penalty term
DrugLogics Pipeline Input Load the DrugLogics pipeline simulation results into R
`get_synergy_scores()`	Get synergy scores from file
`get_model_predictions()`	Load the models predictions data
`get_observed_synergies()`	Load the observed synergies data
`get_stable_state_from_models_dir()`	Load the models stable state data
`get_link_operators_from_models_dir()`	Load the models boolean equation link operator data
`get_fitness_from_models_dir()`	Load the models fitness scores
`get_node_names()`	Get the node names
`get_model_names()`	Get the model names
`get_edges_from_topology_file()`	Get the edges from a specified topology
`construct_network()`	Construct igraph network graph
Confusion Matrix Calculation
`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)
Helpers
`get_observed_model_predictions()`	Subset the model predictions to the (true) observed synergies
`get_unobserved_model_predictions()`	Subset the model predictions to the (false) non-observed synergies
`get_synergy_subset_stats()`	Find the number of predictive models for every synergy subset
`get_synergy_comparison_sets()`	Get synergy comparison sets
`count_models_that_predict_synergies()`	Count models that predict a set of synergies
`get_biomarkers()`	Get total biomarkers from average data differences matrix
`get_biomarkers_per_type()`	Get biomarkers from average data differences matrix (per type)
`is_comb_element_of()`	Is drug combination element of given vector?
`validate_observed_synergies_data()`	Validate observed synergies data
`get_alt_drugname()`	Get alternative drug combination name
`filter_network()`	Filter the network's vertices
`assign_link_operator_value_to_equation()`	Assign link operator value to boolean equation
Plot
`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_graph_vis()`	Plot the graph of average state differences (visNetwork)
`plot_avg_state_diff_graphs()`	Plot the graphs from an average state differences matrix
`plot_mcc_classes_hist()`	Plot histogram of the MCC classes
Print
`print_biomarkers_per_predicted_synergy()`	Print biomarkers for each predicted synergy
`print_model_and_drug_stats()`	Print model and drug statistics

Reference

General

Model Data Differences

DrugLogics Pipeline Input

Confusion Matrix Calculation

Helpers

Plot

Print