bp2.find.nodes: Solve dependencies between pathways and complexes
In microbiome/biopax2: BioPAX level 2 S4 object model

Description Usage Arguments Value Author(s) See Also Examples

Creates a list of nodes and lists of dependencies between the nodes by recursiely traversing given pathways and complexes within the active bp2.model. The collected data includes list of proteins that are directly linked to each pathway and protein and lists of different types of connections between the nodes. These lists can be used ot construct graphs of nodes.

1	nodes <- bp2.find.nodes(pathways, complexes)

`pathways`	List of "bp2.pathway" objects used as nodes. Can be empty.
`complexes`	List of "bp2.complex" objects used as nodes. Can be empty.

Instance of "bp2.nodes" class.

Ossi Koivistoinen

"bp2.nodes", bp2.create.model

my.bp2 <- bp2.create.model(...)
pathways <- bp2.get.instances.of(my.bp2@all.objects, "bp2.pathway")
complexes <- bp2.get.instances.of(my.bp2@all.objects, "bp2.complex")
nodes <- bp2.find.nodes(pathways, complexes)