Man pages for microbiome/biopax2
BioPAX level 2 S4 object model
| bp2.create.model | Construct bp2.model based on RDF data |
| bp2.find | Find bp2 model objects by slot values |
| bp2.find.followers | Construct follower lists for bp2.model objects |
| bp2.find.nodes | Solve dependencies between pathways and complexes |
| bp2.find.proteins | Find UniprotIDs in the list of physical entities |
| bp2.flatten | Flatten lists of lists |
| bp2.get.all.class.names | List BioPAX model class names |
| bp2.get.all.slot.names | List all slot names that are used in bp2 model objects |
| bp2.get.instances.of | Filter particular class from list of objects |
| bp2.get.slot | Read slot values |
| bp2.get.uniprot.ids | Get unitprot ID of a protein object |
| bp2.ids2objects | Convert numeric identifiers of bp2 model objects to S4... |
| bp2.minimum.spanning.tree | Solve minimum spanning trees for follower lists |
| bp2.model-class | bp2.model class: S4 object model of BioPAX level 2 |
| bp2.nodes-class | bp2.nodes class: Connections between pathways |
| bp2.normalize.complexes | Solve proteins that form protein complexes |
| bp2.objects2ids | Convert bp2 model objects to numeric identifiers |
| bp2.resume | Resume saved bp2 model |
| bp2.verbose | Set verbosity of bp2 pacakge |
