Reference

pathfindR

pathfindR package

pathfindR-package pathfindR

pathfindR: A package for Enrichment Analysis Utilizing Active Subnetworks

Main functions

Main functions of pathfindR

run_pathfindR()

Wrapper Function for pathfindR - Active-Subnetwork-Oriented Enrichment Workflow

cluster_enriched_terms()

Cluster Enriched Terms

enrichment_chart()

Create Bubble Chart of Enrichment Results

score_terms()

Calculate Agglomerated Scores of Enriched Terms for Each Subject

plot_scores()

Plot the Heatmap of Score Matrix of Enriched Terms per Sample

term_gene_heatmap()

Create Terms by Genes Heatmap

create_term_gene_graph()

Create Term-Gene Graph

create_term_gene_plot()

Create Term-Gene Plot

UpSet_plot()

Create UpSet Plot of Enriched Terms

visualize_terms()

Create Diagrams for Enriched Terms

cluster_graph_vis()

Graph Visualization of Clustered Enriched Terms

visualize_active_subnetworks()

Visualize Active Subnetworks

Data Generation

Functions to generate PIN and gene sets data

get_pin_file()

Retrieve Organism-specific PIN data

get_gene_sets_list()

Retrieve Organism-specific Gene Sets List

Comparison of 2 pathfindR Results

Functions to compare 2 different pathfindR results

combine_pathfindR_results()

Combine 2 pathfindR Results

combined_results_graph()

Combined Results Graph

Enrichment-related functions

active_snw_enrichment_wrapper()

Wrapper for Active Subnetwork Search + Enrichment over Single/Multiple Iteration(s)

single_iter_wrapper()

Active Subnetwork Search + Enrichment Analysis Wrapper for a Single Iteration

annotate_term_genes()

Annotate the Affected Genes in the Provided Enriched Terms

enrichment()

Perform Enrichment Analysis for a Single Gene Set

enrichment_analyses()

Perform Enrichment Analyses on the Input Subnetworks

fetch_gene_sets()

Fetch Gene Set Objects

hyperg_test()

Hypergeometric Distribution-based Hypothesis Testing

summarize_enrichment_results()

Summarize Enrichment Results

Active Subnetwork Search Functions

Active subnetwork search-related functions

get_active_subnetworks()

Get Active Subnetworks

active_subnetwork_search()

Active subnetwork search

filter_active_subnetworks()

Parse Active Subnetwork Search Output File and Filter the Subnetworks

input_processing()

Process Input

input_testing()

Input Testing

return_pin_path()

Return The Path to Given Protein-Protein Interaction Network (PIN)

build_score_context()

Build the score context

build_network()

Build the undirected interaction network from a SIF file

.greedy_search()

Run the greedy active subnetwork search

.simulated_annealing()

Run the simulated annealing active subnetwork search

.genetic_algorithm()

Run the genetic-algorithm active subnetwork search

.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

.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

.sort_subnetworks_desc()

Sort a list of subnetwork objects by score, descending

example_unfiltered_snws

Example Unfiltered Active Subnetworks

Clustering-related functions

create_kappa_matrix()

Create Kappa Statistics Matrix

fuzzy_term_clustering()

Heuristic Fuzzy Multiple-linkage Partitioning of Enriched Terms

hierarchical_term_clustering()

Hierarchical Clustering of Enriched Terms

Visualization functions

Visualization-related functions

color_kegg_pathway()

Color hsa KEGG pathway

visualize_KEGG_diagram()

Visualize Human KEGG Pathways

visualize_term_interactions()

Visualize Interactions of Genes Involved in the Given Enriched Terms

Misc. functions

Miscellaneous functions

get_biogrid_pin()

Retrieve the Requested Release of Organism-specific BioGRID PIN

process_pin()

Process Data frame of Protein-protein Interactions

get_kegg_gsets()

Retrieve Organism-specific KEGG Pathway Gene Sets

get_reactome_gsets()

Retrieve Reactome Pathway Gene Sets

get_mgsigdb_gsets()

Retrieve Organism-specific MSigDB Gene Sets

gset_list_from_gmt()

Retrieve Gene Sets from GMT-format File

create_HTML_report()

Create HTML Report of pathfindR Results

isColor()

Check if value is a valid color

order_df_by_columnn()

Order input data frame by provided columnn

safe_get_content()

Safely download and parse web content