Man pages for mlist/SPONGE
Sparse Partial Correlations On Gene Expression
| build_classifier_central_genes | build classifiers for central genes |
| calibrate_model | tests and trains a model for a disease using a training and... |
| ceRNA_interactions | ceRNA interactions |
| check_and_convert_expression_data | Checks if expression data is in matrix or ExpressionSet... |
| define_modules | Functions to define Sponge modules, created as all the first... |
| enrichment_modules | Calculate enrichment scores |
| ensembl.df | example potential central nodes |
| filter_ceRNA_network | prepare ceRNA network and network centralities from SPONGE /... |
| fn_combined_centrality | Function to calculate centrality scores Calculation of... |
| fn_discretize_spongeffects | discretize #' (functions taken from: Jerby-Arnon et al. 2018) |
| fn_elasticnet | Computes an elastic net model |
| fn_exact_match_summary | Calibrate classification method |
| fn_filter_network | Preprocessing ceRNA network |
| fn_gene_miRNA_F_test | Perform F test for gene-miRNA elastic net model |
| fn_get_model_coef | Extract the model coefficients from an elastic net model |
| fn_get_rss | Compute the residual sum of squares error for an elastic net... |
| fn_get_semi_random_OE | Function to calculate semi random enrichment scores of... |
| fn_get_shared_miRNAs | Identify miRNAs for which both genes have miRNA binding sites... |
| fn_OE_module | Function to calculate enrichment scores of modules OE... |
| fn_RF_classifier | RF classification model |
| fn_weighted_degree | Function to calculate centrality scores Calculation of... |
| gene_expr | Gene expression test data set |
| genes_pairwise_combinations | Compute all pairwise interactions for a number of genes as... |
| get_central_modules | prepare ceRNA network and network centralities from SPONGE /... |
| mircode_ensg | mircode predicted miRNA gene interactions |
| mircode_symbol | mircode predicted miRNA gene interactions |
| mir_expr | miRNA expression test data set |
| mir_interactions | miRNA / gene interactions |
| plot_accuracy_sensitivity_specificity | list of plots for (1) accuracy and (2) sensitivity +... |
| plot_confusion_matrices | plots the confusion matrix from spongEffects train_and_test()... |
| plot_density_scores | plots the density of the model scores for subtypes (see... |
| plot_heatmaps | plots the heatmaps from training_and_test_model (see Boniolo... |
| plot_involved_miRNAs_to_modules | plots the heatmap of miRNAs invovled in the interactions of... |
| plot_miRNAs_per_gene | plot expression of miRNAs in module for specific RNA (no... |
| plot_target_gene_expressions | plot the target gene heatmap |
| plot_top_modules | plots the top x gini index modules (see Boniolo and Hoffmann... |
| precomputed_cov_matrices | covariance matrices under the null hypothesis that... |
| precomputed_null_model | A null model for testing purposes |
| prepare_metabric_for_spongEffects | prepare METABRIC formats for spongEffects |
| prepare_tcga_for_spongEffects | prepare TCGA formats for spongEffects |
| Random_spongEffects | build random classifiers |
| sample_zero_mscor_cov | Sampling zero multiple miRNA sensitivity covariance matrices |
| sample_zero_mscor_data | Sample mscor coefficients from pre-computed covariance... |
| sponge | Compute competing endogeneous RNA interactions using Sparse... |
| sponge_build_null_model | Build null model for p-value computation |
| sponge_compute_p_values | Compute p-values for SPONGE interactions |
| sponge_edge_centralities | Computes edge centralities |
| sponge_gene_miRNA_interaction_filter | Determine miRNA-gene interactions to be considered in SPONGE |
| sponge_network | Prepare a sponge network for plotting |
| sponge_node_centralities | Computes various node centralities |
| sponge_plot_network | Plot a sponge network |
| sponge_plot_network_centralities | plot node network centralities |
| sponge_plot_simulation_results | Plot simulation results for different null models |
| sponge_run_benchmark | run sponge benchmark where various settings, i.e. with or... |
| sponge_subsampling | Sponge subsampling |
| targetscan_ensg | targetscan predicted miRNA gene interactions |
| targetscan_symbol | targetscan predicted miRNA gene interactions |
| test_cancer_gene_expr | example test expression data for spongEffects |
| test_cancer_metadata | example test sample meta data for spongEffects |
| test_cancer_mir_expr | example test miRNA data for spongEffects |
| train_cancer_gene_expr | example training expression data for spongEffects |
| train_cancer_metadata | example training sample meta data for spongEffects |
| train_cancer_mir_expr | example training miRNA data for spongEffects |
| train_ceRNA_interactions | example train ceRNA interactions for spongEffects |
| train_network_centralities | example train network centralities for spongEffects |
