samplePaths {NetPathMiner} | R Documentation

## Creates a set of sample path p-values for each length given a weighted network

### Description

Randomly traverses paths of increasing lengths within a set network to create an empirical pathway distribution for more accurate determination of path significance.

### Usage

    samplePaths(graph, max.path.length, num.samples = 1000,
      num.warmup = 10, verbose = TRUE)

### Arguments

`graph` | A weighted igraph object. Weights must be in `edge.weights` or `weight` edge attributes.
`max.path.length` | The maxmimum path length.
`num.samples` | The numner of paths to sample
`num.warmup` | The number of warm up paths to sample.
`verbose` | Whether to display the progress of the function.

### Details

Can take a bit of time.

### Value

A matrix where each row is a path length and each column is the number of paths sampled.

### Author(s)

Timothy Hancock

Ahmed Mohamed

### See Also

Other Path ranking methods: `extractPathNetwork`, `getPathsAsEIDs`, `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 significantly correlated paths using "p-valvue" method.
    	##   First, establish path score distribution by calling "samplePaths"
     pathsample <- samplePaths(rgraph, max.path.length=10,
                            num.samples=100, num.warmup=10)

    	##   Get all significant paths with p<0.1
    	significant.p <- pathRanker(rgraph, method = "pvalue",
                    sampledpaths = pathsample ,alpha=0.1)

[Package NetPathMiner version 1.28.0 Index]