Man pages for zgzhao/gmetab
syzMetab: R package for metabolic network analysis
| add.edges | add edges |
| add.reactions | append reaction |
| all_spaths_list | info of all simple paths |
| classes | package class designs |
| delete.edges | delete edges |
| delete.vertices | delete vertices |
| helpers_general | general helper function |
| is.empty | test empty |
| is.kdset | object test |
| KEGG_get | KEGG download API |
| KEGG_ontology | KEGG ontology as data.frame or list |
| kogs_list | KOG to gene mapping list for an organism |
| kogs_table | Gene to KOG mapping table for an organism |
| make_kdset | make metabolic pathway |
| make_mgraph | make graph from various data |
| make_rset | generate ReactionSet object |
| make_stcuts | list all gene cut sets |
| plot.mgraph | plot graph |
| plotReaction | show reaction diagram |
| prob_stcuts | functional probability of s-t gene cutsets |
| rcount | count of graph entities |
| rdata | get/set attribute data |
| rnames | names of graph entities |
| robust | calculate mutational robustness |
| setorg_graph | KO-graph to species-specific graph |
| setorg_path | General to organism-specific KDataSet conversion |
| setorg_stcuts | general (species="ko") stcuts to specices-specific stcuts |
| subset_graph | subset xgraph |
| vis_connected | test connected |
| vs_accessed_by | vertices assessed by given vertices |
| vs_adjacent | adjacent vertices |
