man/extractPathNetwork.Rd
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 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/pathRank.R
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 \name{extractPathNetwork}
 \alias{extractPathNetwork}
 \title{Creates a subnetwork from a ranked path list}
 \usage{
 extractPathNetwork(paths, graph)
 }
 \arguments{
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 \item{paths}{The paths extracted by \code{\link{pathRanker}}.}
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 \item{graph}{A annotated igraph object.}
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 }
 \value{
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 A subnetwork from all paths provided. If paths are computed for several
 labels (sample categories), a subnetwork is returned for each label.
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 }
 \description{
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 Creates a subnetwork from a ranked path list generated by \code{\link{pathRanker}}.
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 }
 \examples{
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 	## Prepare a weighted reaction network.
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 	## 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,
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 		weight.method = "cor", use.attr="miriam.uniprot",
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 		y=factor(colnames(ex_microarray)), bootstrap = FALSE)
 
 	## Get ranked paths using probabilistic shortest paths.
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  ranked.p <- pathRanker(rgraph, method="prob.shortest.path",
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 					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)
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 }
 \seealso{
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 Other Path ranking methods: \code{\link{getPathsAsEIDs}},
   \code{\link{pathRanker}}, \code{\link{samplePaths}}
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 }
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 \author{
 Ahmed Mohamed
 }
 \concept{Path ranking methods}