extractPathNetwork {NetPathMiner} | R Documentation |
Creates a subnetwork from a ranked path list generated by pathRanker
.
extractPathNetwork(paths, graph)
paths |
The paths extracted by |
graph |
A annotated igraph object. |
A subnetwork from all paths provided. If paths are computed for several labels (sample categories), a subnetwork is returned for each label.
Ahmed Mohamed
Other Path ranking methods: getPathsAsEIDs
,
pathRanker
, samplePaths
## Prepare a weighted reaction network. ## Conver a metabolic network to a reaction network. data(ex_sbml) # bipartite metabolic network of Carbohydrate metabolism. rgraph <- makeReactionNetwork(ex_sbml, simplify=TRUE) ## Assign edge weights based on Affymetrix attributes and microarray dataset. # Calculate Pearson's correlation. data(ex_microarray) # Part of ALL dataset. rgraph <- assignEdgeWeights(microarray = ex_microarray, graph = rgraph, weight.method = "cor", use.attr="miriam.uniprot", y=factor(colnames(ex_microarray)), bootstrap = FALSE) ## Get ranked paths using probabilistic shortest paths. ranked.p <- pathRanker(rgraph, method="prob.shortest.path", K=20, minPathSize=6) ## Get the subnetwork of paths in reaction graph. reaction.sub <- getPathsAsEIDs(ranked.p, rgraph) ## Get the subnetwork of paths in the original metabolic graph. metabolic.sub <- getPathsAsEIDs(ranked.p, ex_sbml)