extractPathNetwork: Creates a subnetwork from a ranked path list

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

Creates a subnetwork from a ranked path list

Description

Creates a subnetwork from a ranked path list generated by pathRanker.

Usage

extractPathNetwork(paths, graph)

Arguments

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

Value

A subnetwork from all paths provided. If paths are computed for several labels (sample categories), a subnetwork is returned for each label.

Author(s)

Ahmed Mohamed

See Also

Other Path ranking methods: getPathsAsEIDs, 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 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)

ahmohamed/NetPathMiner documentation built on May 15, 2023, 12:53 p.m.