Enrichment Analysis Utilizing Active Subnetworks
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Documentation for package ‘pathfindR’ version 3.0.0
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| pathfindR-package | pathfindR: A package for Enrichment Analysis Utilizing Active Subnetworks |
| .find_components_named | Find the connected components among a set of "on" nodes |
| .find_subnetworks | Find the scored subnetworks among a set of "on" nodes |
| .ga_compare | Compare two individuals rank-by-rank |
| .ga_crossover_mutation | Crossover and mutation of two parent genomes |
| .ga_make_individual | Build a GA individual from a logical genome |
| .ga_pick | Pick one index by rank-proportional (roulette) selection |
| .ga_score | Fitness of an individual |
| .ga_sort_desc | Sort a population from best to worst |
| .genetic_algorithm | Run the genetic-algorithm active subnetwork search |
| .greedy_search | Run the greedy active subnetwork search |
| .make_subnetwork | Create a subnetwork object from a vector of node names |
| .parse_experiment | Parse the experiment input into a clean gene / p-value data frame |
| .score_subnetwork | Score a subnetwork from its size and z-score sum |
| .simulated_annealing | Run the simulated annealing active subnetwork search |
| .sort_subnetworks_desc | Sort a list of subnetwork objects by score, descending |
| active_snw_enrichment_wrapper | Wrapper for Active Subnetwork Search + Enrichment over Single/Multiple Iteration(s) |
| active_subnetwork_search | Active subnetwork search |
| annotate_term_genes | Annotate the Affected Genes in the Provided Enriched Terms |
| build_network | Build the undirected interaction network from a SIF file |
| build_score_context | Build the score context |
| cluster_enriched_terms | Cluster Enriched Terms |
| cluster_graph_vis | Graph Visualization of Clustered Enriched Terms |
| color_kegg_pathway | Color hsa KEGG pathway |
| combined_results_graph | Combined Results Graph |
| combine_pathfindR_results | Combine 2 pathfindR Results |
| create_HTML_report | Create HTML Report of pathfindR Results |
| create_kappa_matrix | Create Kappa Statistics Matrix |
| create_term_gene_graph | Create Term-Gene Graph |
| create_term_gene_plot | Create Term-Gene Plot |
| enrichment | Perform Enrichment Analysis for a Single Gene Set |
| enrichment_analyses | Perform Enrichment Analyses on the Input Subnetworks |
| enrichment_chart | Create Bubble Chart of Enrichment Results |
| example_unfiltered_snws | Example Unfiltered Active Subnetworks |
| fetch_gene_sets | Fetch Gene Set Objects |
| filter_active_subnetworks | Parse Active Subnetwork Search Output File and Filter the Subnetworks |
| fuzzy_term_clustering | Heuristic Fuzzy Multiple-linkage Partitioning of Enriched Terms |
| get_active_subnetworks | Get Active Subnetworks |
| get_biogrid_pin | Retrieve the Requested Release of Organism-specific BioGRID PIN |
| get_gene_sets_list | Retrieve Organism-specific Gene Sets List |
| get_kegg_gsets | Retrieve Organism-specific KEGG Pathway Gene Sets |
| get_mgsigdb_gsets | Retrieve Organism-specific MSigDB Gene Sets |
| get_pin_file | Retrieve Organism-specific PIN data |
| get_reactome_gsets | Retrieve Reactome Pathway Gene Sets |
| gset_list_from_gmt | Retrieve Gene Sets from GMT-format File |
| hierarchical_term_clustering | Hierarchical Clustering of Enriched Terms |
| hyperg_test | Hypergeometric Distribution-based Hypothesis Testing |
| input_processing | Process Input |
| input_testing | Input Testing |
| isColor | Check if value is a valid color |
| order_df_by_columnn | Order input data frame by provided columnn |
| pathfindR | pathfindR: A package for Enrichment Analysis Utilizing Active Subnetworks |
| plot_scores | Plot the Heatmap of Score Matrix of Enriched Terms per Sample |
| process_pin | Process Data frame of Protein-protein Interactions |
| return_pin_path | Return The Path to Given Protein-Protein Interaction Network (PIN) |
| run_pathfindR | Wrapper Function for pathfindR - Active-Subnetwork-Oriented Enrichment Workflow |
| safe_get_content | Safely download and parse web content |
| score_terms | Calculate Agglomerated Scores of Enriched Terms for Each Subject |
| single_iter_wrapper | Active Subnetwork Search + Enrichment Analysis Wrapper for a Single Iteration |
| summarize_enrichment_results | Summarize Enrichment Results |
| term_gene_heatmap | Create Terms by Genes Heatmap |
| UpSet_plot | Create UpSet Plot of Enriched Terms |
| visualize_active_subnetworks | Visualize Active Subnetworks |
| visualize_KEGG_diagram | Visualize Human KEGG Pathways |
| visualize_terms | Create Diagrams for Enriched Terms |
| visualize_term_interactions | Visualize Interactions of Genes Involved in the Given Enriched Terms |