getGraphEntryGenes: Extract all the possible entry point (genes with no entering...
In clipper: Gene Set Analysis Exploiting Pathway Topology

Description Usage Arguments Value References Examples

It extracts the possible entry point of the graph. Entry points are defined as nodes with no entering edges.

1	getGraphEntryGenes(graph, byCliques=FALSE, root=NULL)

`graph`	a `graphNEL` object.
`byCliques`	when TRUE it returns a list where entry point are organized by cliques.
`root`	nodes by which rip ordering is performed (as far as possible) on the variables using the maximum cardinality search algorithm.

a vector of gene names representing the entry point of 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"))
  getGraphEntryGenes(graph)
}