% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/pathRank.R

 \name{extractPathNetwork}
 \alias{extractPathNetwork}
 \title{Creates a subnetwork from a ranked path list}
 \usage{
 extractPathNetwork(paths, graph)
 }
 \arguments{

 \item{paths}{The paths extracted by \code{\link{pathRanker}}.}

 \item{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.

 }
 \description{

 Creates a subnetwork from a ranked path list generated by \code{\link{pathRanker}}.

 }
 \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)

 }
 \seealso{

 Other Path ranking methods: \code{\link{getPathsAsEIDs}},
   \code{\link{pathRanker}}, \code{\link{samplePaths}}

 }

 \author{
 Ahmed Mohamed
 }
 \concept{Path ranking methods}