Enrichment Analysis Utilizing Active Subnetworks


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Documentation for package ‘pathfindR’ version 1.4.2

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active_snw_search Perform Active Subnetwork Search
annotate_term_genes Annotate the Affected Genes in the Provided Enriched Terms
biocarta_descriptions BioCarta Pathways - Descriptions
biocarta_genes BioCarta Pathways - Gene Sets
biogrid_adj_list BioGRID PIN Adjacency List
check_java_version Check Java Version
cluster_enriched_terms Cluster Enriched Terms
cluster_graph_vis Graph Visualization of Clustered Enriched Terms
color_kegg_pathway Color hsa KEGG pathway
create_kappa_matrix Create Kappa Statistics Matrix
custom_result Custom Gene Set Enrichment Results
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_active_snws Example Active Subnetworks
fetch_gene_set Fetch Gene Set Objects
fetch_java_version Obtain Java Version
filterActiveSnws Parse Active Subnetwork Search Output File and Filter the Subnetworks
fuzzy_term_clustering Heuristic Fuzzy Multiple-linkage Partitioning of Enriched Terms
genemania_adj_list GeneMania PIN Adjacency List
go_all_genes Gene Ontology - All Gene Ontology Gene Sets
GO_all_terms_df Gene Ontology - All Gene Ontology Descriptions
hierarchical_term_clustering Hierarchical Clustering of Enriched Terms
hyperg_test Hypergeometric Distribution-based Hypothesis Testing
input_processing Process Input
input_testing Input Testing
intact_adj_list IntAct PIN Adjacency List
kegg_adj_list KEGG PIN Adjacency List
kegg_descriptions KEGG Pathways - Descriptions
kegg_genes KEGG Pathways - Gene Sets
mmu_kegg_descriptions Mus Musculus KEGG Pathways - Descriptions
mmu_kegg_genes Mus Musculus KEGG Pathways - Gene Sets
mmu_string_adj_list Mus musculus STRING PIN Adjacency List
myeloma_input Example Input for Myeloma Analysis (Mus Musculus)
myeloma_output Example Output for Myeloma Analysis (Mus Musculus)
pathfindR pathfindR: A package for Enrichment Analysis Utilizing Active Subnetworks
plot_scores Plot the Heatmap of Score Matrix of Enriched Terms per Sample
RA_clustered Example Output for the pathfindR Clustering Workflow - Rheumatoid Arthritis
RA_exp_mat Example Input for pathfindR - Enriched Term Scoring
RA_input Example Input for the pathfindR Enrichment Workflow - Rheumatoid Arthritis
RA_output Example Output for the pathfindR Enrichment Workflow - Rheumatoid Arthritis
reactome_descriptions Reactome Pathways - Descriptions
reactome_genes Reactome Pathways - Gene Sets
return_pin_path Return The Path to Given Protein-Protein Interaction Network (PIN)
run_pathfindR Wrapper Function for pathfindR - Active-Subnetwork-Oriented Enrichment Analysis
score_terms Calculate Agglomerated Scores of Enriched Terms for Each Subject
string_adj_list STRING PIN Adjacency List
summarize_enrichment_results Summarize Enrichment Results
term_gene_graph Plot Term-Gene Graph
visualize_hsa_KEGG Visualize Human KEGG Pathways
visualize_terms Create Diagrams for Enriched Terms
visualize_term_interactions Visualize Interactions of Genes Involved in the Given Enriched Terms