extractPathNetwork {NetPathMiner} | R Documentation

## 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)

[Package NetPathMiner version 1.16.0 Index]