getGraphEntryGenes {clipper} | R Documentation |
It extracts the possible entry point of the graph. Entry points are defined as nodes with no entering edges.
getGraphEntryGenes(graph, byCliques=FALSE, root=NULL)
graph |
a |
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) }