\donttest{} instead of
\dontrun{}, as requested by CRAN.mg_string_species() now returns the documented taxon_id column: the
leading # of the STRING #taxon_id header is stripped instead of being
kept in the column name.Initial release of the mechanism evidence graph data model. Built
demand-driven: the first real consumer is the NSEA workflow
(clusterProfiler::nseGO() / ReactomePA::nsePathway()), which now
accepts a mechgraph network through enrichit::prepare_network().
mg_graph(), mg_empty(), mg_validate(), is_mechgraph():
construct and validate a mechgraph object (nodes/edges/metadata
base data.frame tables).mg_nodes(), mg_edges(), mg_metadata(), mg_sources().mg_add_nodes(), mg_add_edges(), mg_drop_nodes(),
mg_drop_edges(), mg_bind(), mg_combine().mg_filter_nodes(), mg_filter_edges(),
mg_induced_subgraph().mg_from_edges(), coercion as_mechgraph().mg_qc().mg_from_string(): download and map a STRING functional or physical
network (protein.links / protein.physical.links) into a mechgraph
with type = "ppi" edges carrying the STRING combined score and full
provenance metadata.protein.aliases table:
keytype = "entrez" (default), "symbol", "uniprot",
"ensembl_gene", "ensembl_protein", "string_id".mg_string_versions(), mg_string_file_url(),
mg_string_download() (cached), mg_string_parse(),
mg_string_species().mg_from_biogrid(): download and parse BioGRID multi-validated
physical interactions (TAB3/MITAB) into a mechgraph with
type = "ppi" edges.mg_biogrid_versions(), mg_biogrid_file_url(),
mg_biogrid_download() (cached), mg_biogrid_parse().