# Enrichment Analysis Utilizing Active Subnetworks

## Documentation for package ‘pathfindR’ version 3.0.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

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