getPathsAsEIDs: Convert a ranked path list to edge ids of a graph

In aiminy/NetPathMiner: NetPathMiner for Biological Network Construction, Path Mining and Visualization

Description

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).

Usage

getPathsAsEIDs(paths, graph)

Arguments

paths	The paths extracted by pathRanker.
graph	A annotated igraph object.

Value

A list of edge ids on the provided graph.

Author(s)

Ahmed Mohamed

See Also

Other Path ranking methods: extractPathNetwork, pathRanker, samplePaths

Examples

	## 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)

aiminy/NetPathMiner documentation built on May 12, 2019, 3:38 a.m.