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NCIgraph (version 1.20.0)

Pathways from the NCI Pathways Database

Description

Provides various methods to load the pathways from the NCI Pathways Database in R graph objects and to re-format them.

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Version

Version

1.20.0

License

GPL-3

Maintainer

Laurent Jacob

Last Published

February 15th, 2017

Functions in NCIgraph (1.20.0)

NCI.demo.cyList

10 raw NCI networks from Nature curated pathways and BioCarta imported as graphNEL objects, for demonstration purpose
directedBFS

Uses a breadth first search on a directed graph to identify which genes are regulated by a particular node in the graph
is.NCIgraph

Assess whether a graph is a NCI graph
getNCIPathways

Loads networks from Cytoscape and parses them
edgesToMerge

Identifies edges that should be merged to parse a NCI network
parseNCInetwork

Takes a NCI network and transforms it into a simpler graph only representing inhibition/activation relationships between genes
mergeNodes

Merges a given list of nodes in a graph
NCIgraph

Class NCIgraph
translateNCI2GeneID

Gives the entrezID corresponding to the nodes of a graph
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
getSubtype.NCIgraph

Returns a list of @KEGGEdgeSubType objects describing each edge of the NCI network