Package: mechgraph 0.0.1
mechgraph: Mechanism Evidence Graph Data Model
Provides a lightweight graph data model for representing, combining, querying, and summarizing evidence-backed biological mechanism graphs. A mechgraph is an S3 list holding a node table, an edge table, and provenance metadata. The package implements builders that convert STRING and BioGRID interaction tables into mechgraph objects, combiners (mg_bind(), mg_combine()) that merge graphs while preserving duplicate evidence records, accessors (mg_nodes(), mg_edges(), mg_metadata()) and mutators (mg_add_*(), mg_drop_*()) for node and edge tables, filters by type, source, identifier, and score, induced-subgraph construction, structural validation (mg_validate()), and quality-control summaries (mg_qc()). Szklarczyk et al. (2023) <doi:10.1093/nar/gkac1000> Oughtred et al. (2021) <doi:10.1002/pro.3938>.
Authors:
mechgraph_0.0.1.tar.gz
mechgraph_0.0.1.zip(r-4.7-any)mechgraph_0.0.1.zip(r-4.6-any)mechgraph_0.0.1.zip(r-4.5-any)
mechgraph_0.0.1.tgz(r-4.6-any)mechgraph_0.0.1.tgz(r-4.5-any)
mechgraph_0.0.1.tar.gz(r-4.7-any)mechgraph_0.0.1.tar.gz(r-4.6-any)
mechgraph_0.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
mechgraph/json (API)
| # Install 'mechgraph' in R: |
| install.packages('mechgraph', repos = c('https://guangchuangyu.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:fb6b301f70. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 123 | ||
| source / vignettes | OK | 209 | ||
| linux-release | OK | 124 | ||
| macos-release | OK | 87 | ||
| macos-oldrel | OK | 75 | ||
| windows-devel | OK | 70 | ||
| windows-release | OK | 60 | ||
| windows-oldrel | OK | 63 | ||
| wasm-release | OK | 111 |
Exports:as_mechgraphis_mechgraphmg_add_edgesmg_add_nodesmg_bindmg_biogrid_downloadmg_biogrid_file_urlmg_biogrid_parsemg_biogrid_versionsmg_combinemg_drop_edgesmg_drop_nodesmg_edgesmg_emptymg_filter_edgesmg_filter_nodesmg_from_biogridmg_from_edgesmg_from_stringmg_graphmg_induced_subgraphmg_metadatamg_nodesmg_qcmg_sourcesmg_string_downloadmg_string_file_urlmg_string_parsemg_string_speciesmg_string_versionsmg_validate
Dependencies:clicpp11glueigraphlatticelifecyclemagrittrMatrixpkgconfigrlangvctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Convert a mechgraph object to an igraph object | as.igraph.mechgraph |
| Modify mechgraph nodes and edges | mg_add_edges mg_add_nodes mg_drop_edges mg_drop_nodes |
| Combine mechgraph objects | mg_bind mg_combine |
| Filter mechgraph objects | mg_filter_edges mg_filter_nodes mg_induced_subgraph |
| Build a mechgraph from BioGRID | mg_biogrid_download mg_biogrid_file_url mg_biogrid_parse mg_biogrid_versions mg_from_biogrid |
| Build a mechgraph from an edge list | as_mechgraph mg_from_edges |
| Build a mechgraph from STRING | mg_from_string mg_string_download mg_string_file_url mg_string_parse mg_string_species mg_string_versions |
| Create and inspect mechgraph objects | is_mechgraph mg_empty mg_graph |
| Access mechgraph tables and metadata | mg_edges mg_metadata mg_nodes mg_sources |
| Summarize mechgraph quality-control metrics | mg_qc |
| Validate a mechgraph object | mg_validate |