man/getPathsAsEIDs.Rd
2aadfaf5
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/pathRank.R
96e22bfc
 \name{getPathsAsEIDs}
 \alias{getPathsAsEIDs}
 \title{Convert a ranked path list to edge ids of a graph}
 \usage{
 getPathsAsEIDs(paths, graph)
 }
 \arguments{
a6b3c979
 \item{paths}{The paths extracted by \code{\link{pathRanker}}.}
96e22bfc
 
a6b3c979
 \item{graph}{A annotated igraph object.}
96e22bfc
 }
 \value{
 A list of edge ids on the provided graph.
 }
 \description{
a6b3c979
 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).
96e22bfc
 }
 \examples{
2aadfaf5
 	## Prepare a weighted reaction network.
96e22bfc
 	## 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,
087265c8
 		weight.method = "cor", use.attr="miriam.uniprot",
96e22bfc
 		y=factor(colnames(ex_microarray)), bootstrap = FALSE)
 
 	## Get ranked paths using probabilistic shortest paths.
087265c8
  ranked.p <- pathRanker(rgraph, method="prob.shortest.path",
96e22bfc
 					K=20, minPathSize=6)
087265c8
 
96e22bfc
 	## 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)
2aadfaf5
 
96e22bfc
 }
 \seealso{
2aadfaf5
 Other Path ranking methods: \code{\link{extractPathNetwork}},
   \code{\link{pathRanker}}, \code{\link{samplePaths}}
96e22bfc
 }
087265c8
 \author{
 Ahmed Mohamed
 }
 \concept{Path ranking methods}