getPathsAsEIDs {NetPathMiner} | R Documentation |
Convert a ranked path list to Edge ids of a graph, where paths can come from a different representation (for example matching path from a reaction network to edges on a metabolic network).
getPathsAsEIDs(paths, graph)
paths |
The paths extracted by |
graph |
A annotated igraph object. |
A list of edge ids on the provided graph.
Ahmed Mohamed
Other Path ranking methods: extractPathNetwork
,
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 edge ids along paths in the reaction graph. path.eids <- getPathsAsEIDs(ranked.p, rgraph) ## Get the edge ids along paths in the original metabolic graph. path.eids <- getPathsAsEIDs(ranked.p, ex_sbml)