directedBFS |
Uses a breadth first search on a directed graph to identify which genes are regulated by a particular node in the graph |
edgesToMerge |
Identifies edges that should be merged to parse a NCI network |
getNCIPathways |
Loads networks from Cytoscape and parses them |
getSubtype.NCIgraph |
Returns a list of @KEGGEdgeSubType objects describing each edge of the NCI network |
is.NCIgraph |
Assess whether a graph is a NCI graph |
mergeNodes |
Merges a given list of nodes in a graph |
NCI.demo.cyList |
10 raw NCI networks from Nature curated pathways and BioCarta imported as graphNEL objects, for demonstration purpose |
NCIgraph-class |
Class NCIgraph |
parseNCInetwork |
Takes a NCI network and transforms it into a simpler graph only representing inhibition/activation relationships between genes |
propagateRegulation |
Transforms the network in a way that each Biochemical Reaction node pointing to a Complex points to what is regulated by the complex and updates the interaction types accordingly |
translateNCI2GeneID |
Gives the entrezID corresponding to the nodes of a graph |