getJunctionTreePaths: Extract the shortest paths along the junction tree of the...
In clipper: Gene Set Analysis Exploiting Pathway Topology

Description Usage Arguments Value References Examples

Find the shortest paths in the Junction tree designed with the cliques of the graph.

1	getJunctionTreePaths(graph, root=NULL)

`graph`	a `graphNEL` object.
`root`	nodes by which rip ordering is performed (as far as possible) on the variables using the maximum cardinality search algorithm.

list of clique indices representing the shortest paths of the graph.

Martini P, Sales G, Massa MS, Chiogna M, Romualdi C. Along signal paths: an empirical gene set approach exploiting pathway topology. NAR. 2012 Sep.

Massa MS, Chiogna M, Romualdi C. Gene set analysis exploiting the topology of a pathway. BMC System Biol. 2010 Sep 1;4:121.

if (require(graphite)) {
  kegg  <- pathways("hsapiens", "kegg")
  graph <- pathwayGraph(convertIdentifiers(kegg$'Chronic myeloid leukemia', "entrez"))
  getJunctionTreePaths(graph)
}