bp2.nodes-class: bp2.nodes class: Connections between pathways
In microbiome/biopax2: BioPAX level 2 S4 object model

Description Objects from the class Slots Author(s) See Also

Description of connections between pathways and protein complexes. The objects of this class contain many lists whose members are either vectors of UniprotIDs or indexes of nodes within this object.

With the exception of inverse.proteins all list are of same length and position in the list is the index of the node. The bp2 model indexes and names of nodes are found in ids table.

Returned by bp2.find.nodes function.

ids: List of numeric numeric bp2 model id of objects. The numbers in all other lis are indexes of this list. Thus, this list can be used to find corresponding objects in bp2.all.objects table
proteins: List of character vectors of Uniprot IDs in this particular node
inverse.proteins: Special list whose indexes are all uniprot IDs that appear in the model and values are list of node indexes that contain the protein
sub.nodes: List of vectors of other node indexes that are included in the nodes.
nodes.with.common.proteins: List of vectors of other node indexes that share proteins with the nodes.
nodes.with.activated.proteins: List of vectors of other node indexes that are share protein through activation relation with the nodes.
nodes.with.inhibited.proteins: List of vectors of other node indexes that are share protein through inhibition relation with the nodes.
activated.nodes: List of vectors of other node indexes that are activated by the nodes.
activated.proteins: List of character vectors Uniprot IDs that are activated by the nodes.
inhibited.nodes: List of of other node indexes that are inhibited by the nodes.
inhibited.proteins: List of character vectors Uniprot IDs that are inhibited by the nodes.
all.followers: Union of sub.nodes, activated.nodes, inhibited.nodes and common.proteins
all.inhibited: Union of inhibited.nodes and nodes.with.inhibited.protein