writeEdges: Output network edges to text in Cytoscape-readable format.

Description

Outputs a data frame of probabilistic network edges to a text file suitable as input to Cytoscape for visualization.

Usage

writeEdges( network, threshhold = .5, fileName = "edges.txt")

Arguments

network

A network represented as a data frame in which each row corresponds to an edge for which the probability is estimated to be nonzero. The first column gives the name of the regulator, the second column gives the name of the regulated gene, and the third column gives the estimated probability for the regulator-gene pair.

threshhold

A threshhold on the probability that the variables in x. The default value is .5

fileName

A character string given the desired name of the output text file. The default is "edges.txt".

Value

The data frame of edges with those having probabilities below the specified threshhold removed. As a side effect, this data from is output to a text file named fileName in a format suitable for use with Cytoscape for visualization (see www.cytoscape.org).

References

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003), Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research 13:2498-504

Examples

Run this code

data(dream4)

network <- 1

nTimePoints <- length(unique(dream4ts10[[network]]$time))

edges1ts10 <- networkBMA( data = dream4ts10[[network]][,-(1:2)], 
                          nTimePoints = nTimePoints, prior.prob = 0.1)

writeEdges(edges1ts10)