Version checked for this guide: 1.0.10 · 2026-09-23
For compound-level enrichment, prepare de-duplicated compound IDs, a pathway database for the organism and an explicit selection rule. Match KEGG IDs to KEGG resources and HMDB IDs to compatible resources; human-readable names are not a substitute for these identifiers.
enrich_kegg(), enrich_hmdb() and enrich_pathways() support the documented pathway enrichment interfaces. Specify the adjustment method instead of silently accepting a default. In enrich_kegg(), the background derives from the supplied pathway database; the interface does not expose a separate background argument. If your experiment requires a measured-compound universe, construct and verify an appropriately restricted database or use a method with an explicit universe. Do not silently report the full database as the measured background.
Feature-based functionality includes isotope annotation, RT grouping, candidate assignment, activity scoring, null distributions and perform_fpa(). It extends analysis beyond confidently annotated compounds while retaining annotation uncertainty. Such modules are hypotheses, not confirmation of every compound or pathway activity. Bar, scatter and network displays summarize supported results.
Functional scope
Pathway data access/filtering; over-representation tests; enrichment plots/networks; isotope/feature grouping and functional module analysis.
Example
# Requires your deduplicated IDs and a pathway_database object.
# enrichment <- metpath::enrich_kegg(
# query_id = unique(selected_kegg_ids), query_type = "compound",
# id_type = "KEGG", pathway_database = pathway_database,
# method = "hypergeometric", p_adjust_method = "BH",
# p_cutoff = 0.05, threads = 2
# )
help("perform_fpa", package = "metpath")
Find a function
The checked source exports the following APIs, including compatibility interfaces and utilities. Consult the installed version with help("function_name", package = "metpath") for argument details.
Show exported functions
annotate_isotope, annotate_metabolites_fpa, arrange, calculate_activity_score, calculate_activity_socre, calculate_centrality, calculate_redundance, compound_list, database_info, describtion, enrich_bar_plot, enrich_hmdb, enrich_kegg, enrich_metabolic_pathway, enrich_network, enrich_pathways, enrich_scatter_plot, filter, filter_pathway, gene_list, generate_null_activity_score_distribution, get_hidden_metabolites, get_pathway_class, group_peaks_rt, identify_metabolic_modules, metpath_conflicts, metpath_logo, metpath_packages, pathway_class, pathway_id, pathway_name, perform_fpa, plot_metabolic_module_fpa, plot_metabolic_network_fpa, reference_list, related_disease, related_module, remove_redundancy, score_peak_group
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