Man pages for emba
Ensemble Boolean Model Biomarker Analysis

add_numbers_above_the_barsAdd numbers horizontally above the bars of a barplot
assign_link_operator_value_to_equationAssign link operator value to boolean equation
biomarker_mcc_analysisBiomarker analysis based on MCC model classification
biomarker_synergy_analysisBiomarker analysis per synergy predicted
biomarker_tp_analysisBiomarker analysis based on TP model classification
calculate_mccCalculate the Matthews correlation coefficient vector
calculate_models_mccCalculate the Matthews correlation coefficient for each model
calculate_models_synergies_fnCount the non-synergies of the observed synergies per model...
calculate_models_synergies_fpCount the predictions of the non-synergistic drug...
calculate_models_synergies_tnCount the non-synergies of the non-synergistic drug...
calculate_models_synergies_tpCount the predictions of the observed synergies per model...
construct_networkConstruct igraph network graph
count_models_that_predict_synergiesCount models that predict a set of synergies
embaemba
filter_networkFilter the network's vertices
get_alt_drugnameGet alternative drug combination name
get_avg_activity_diff_based_on_mcc_clusteringGet the average activity difference based on MCC clustering
get_avg_activity_diff_based_on_specific_synergy_predictionGet average activity difference based on specific synergy...
get_avg_activity_diff_based_on_synergy_set_cmpGet the average activity difference based on the comparison...
get_avg_activity_diff_based_on_tp_predictionsGet the average activity difference based on the number of...
get_avg_activity_diff_mat_based_on_mcc_clusteringGet average activity difference matrix based on MCC...
get_avg_activity_diff_mat_based_on_specific_synergy_predictionGet average activity difference matrix based on specific...
get_avg_activity_diff_mat_based_on_tp_predictionsGet average activity difference matrix based on the number of...
get_avg_link_operator_diff_based_on_specific_synergy_predictionGet average link operator difference based on specific...
get_avg_link_operator_diff_based_on_synergy_set_cmpGet the average link operator difference based on the...
get_avg_link_operator_diff_mat_based_on_mcc_clusteringGet average link operator difference matrix based on MCC...
get_avg_link_operator_diff_mat_based_on_specific_synergy_predictionGet average link operator difference matrix based on specific...
get_avg_link_operator_diff_mat_based_on_tp_predictionsGet average link operator difference matrix based on the...
get_biomarkersGet total biomarkers from average data differences matrix
get_biomarkers_per_typeGet biomarkers from average data differences matrix (per...
get_edges_from_topology_fileGet the edges from a specified topology
get_fitness_from_models_dirLoad the models fitness scores
get_link_operators_from_models_dirLoad the models boolean equation link operator data
get_model_namesGet the model names
get_model_predictionsLoad the models predictions data
get_models_based_on_mcc_class_idGet models based on the MCC class id
get_neighborsGet neighbor nodes
get_node_colorsGet the node colors
get_node_namesGet the node names
get_observed_model_predictionsSubset the model predictions to the (true) observed synergies
get_observed_synergiesLoad the observed synergies data
get_observed_synergies_per_cell_lineGet observed synergies per cell line
get_perf_biomarkers_per_cell_lineGet performance biomarkers per cell line
get_stable_state_from_models_dirLoad the models stable state data
get_synergy_biomarkers_from_dirGet synergy biomarkers from dir
get_synergy_biomarkers_per_cell_lineGet synergy biomarkers per cell line
get_synergy_comparison_setsGet synergy comparison sets
get_synergy_subset_statsFind the number of predictive models for every synergy subset
get_unobserved_model_predictionsSubset the model predictions to the (false) non-observed...
get_x_axis_valuesGet the refined x-axis values
is_comb_element_ofIs drug combination element of given vector?
make_barplot_on_models_statsBar plot of model stats
make_barplot_on_synergy_subset_statsBar plot of observed synergy subsets
plot_avg_link_operator_diff_graphPlot the graph of average link operator differences (igraph)
plot_avg_link_operator_diff_graphsPlot the graphs from an average link operator differences...
plot_avg_state_diff_graphPlot the graph of average state differences (igraph)
plot_avg_state_diff_graphsPlot the graphs from an average state differences matrix
plot_avg_state_diff_graph_visPlot the graph of average state differences (visNetwork)
plot_mcc_classes_histPlot histogram of the MCC classes
print_biomarkers_per_predicted_synergyPrint biomarkers for each predicted synergy
print_model_and_drug_statsPrint model and drug statistics
update_biomarker_filesUpdate biomarker files for a specific synergy
validate_observed_synergies_dataValidate observed synergies data
emba documentation built on March 26, 2020, 7:13 p.m.