Pathways from the NCI Pathways Database


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Documentation for package ‘NCIgraph’ version 1.0.0

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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