Retrieves pathway to metabolite mappings from WikiPathways (via
wikipathways_metabolites_sparql()) via OmnipathR and returns a long-format table with
one metabolite identifier per row.
Usage
metsigdb_wikipathways(species = "Homo sapiens", exclude_metabolites = "all")
Arguments
- species
Character. Species name. Default is "Homo sapiens".
- exclude_metabolites
Optional metabolite classes to exclude:
NULL (exclude nothing), "all" (default), or any combination of
c("ions", "small_molecules", "xenobiotics", "atoms").
Value
A tibble in long format with columns pathway_id, pathway_name,
pathway_url, n_metabolites_in_pathway, and metabolite_id.