enrichmet: R package for Quick and Easy Pathway and Network Analyses in Metabolomics

Documentation for package ‘enrichmet’ version 0.99.18

calculate_metabolite_centrality	Calculate Metabolite Centrality
create_centrality_plot	Create Centrality Plot
create_enrichment_plot	Create Pathway Enrichment Plot
create_gsea_plot	Create GSEA Plot
create_heatmap_plot	Create Enrichment Heatmap
create_impact_plot	Create Impact vs Significance Plot
create_interaction_plot	Create Metabolite Interaction Network (Reactome)
create_membership_plot	Create Pathway Membership Plot
create_network_plot	Create Metabolite Pathway Network
da_results_from_se	Convert a SummarizedExperiment to a da_results Object
enrichmet	ENRICHMET: Comprehensive Pathway Analysis for Metabolomics Data
extract_kegg_ids	Extract KEGG compound IDs from pathway data
extract_measured_kegg_ids	Extract measured KEGG metabolite IDs from a summary statistics table
fetch_kegg_chebi	Fetch KEGG-ChEBI mappings
fetch_kegg_compound_lookup	Fetch KEGG compound names
fetch_kegg_pathway_metabolites	Fetch KEGG pathway-metabolite relationships
fetch_kegg_reactome	Build KEGG-Reactome reaction mappings
fetch_lion_lipid_ontology	Fetch LION lipid ontology
fetch_reactome_reactions	Fetch Reactome reactions
get_cached_file	Download and cache a remote file
perform_enrichment_analysis	Perform Pathway Enrichment Analysis
perform_enrichment_analysis_bg	Perform pathway enrichment with optional background correction
perform_gsea_analysis	Perform GSEA-style Pathway Enrichment Analysis
prepare_gmt_data	Prepare GMT Data for Pathway Analysis
run_de	Run Differential Expression Analysis using LIMMA