mechgraph 0.0.1

CRAN resubmission

• Examples that download data now use \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().

Core container

• mg_graph(), mg_empty(), mg_validate(), is_mechgraph(): construct and validate a mechgraph object (nodes/edges/metadata base data.frame tables).
• Accessors mg_nodes(), mg_edges(), mg_metadata(), mg_sources().
• Mutators mg_add_nodes(), mg_add_edges(), mg_drop_nodes(), mg_drop_edges(), mg_bind(), mg_combine().
• Filters mg_filter_nodes(), mg_filter_edges(), mg_induced_subgraph().
• Builder mg_from_edges(), coercion as_mechgraph().
• QC summary mg_qc().

STRING backend

• 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.
• Identifier mapping through the STRING 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().

BioGRID backend

• 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().