clipper (version 1.12.0)

getGraphEntryGenes: Extract all the possible entry point (genes with no entering edges) from graph.

Description

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

Usage

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

Arguments

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.

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"))
  getGraphEntryGenes(graph)
}