clipper (version 1.12.0)

getJunctionTreePaths: Extract the shortest paths along the junction tree of the graph.

Description

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

Usage

getJunctionTreePaths(graph, root=NULL)

Arguments

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.

Value

References

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.

Examples

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