gasub

R package for extraction of active subnetworks using a global search algorithm

Installation

The package has been tested on OSX and Unix systems.

Installing Julia

Computationally intensive tasks of GASUB are implemented in Julia. Currently, the package requires Julia v0.4.6

Additionally, the following Julia packages are required:

Pkg.add("Distributions")
Pkg.add("JSON")
Pkg.add("LightGraphs")

Pkg.update()

Installing the R package

devtools::install_git("https://github.com/idroz/gasub")

Usage

library(gasub)
library(igraph)

g <- graph.lattice(dimvector = c(5,6))
V(g)$name <- seq_len(vcount(g))
weights <- runif(n = vcount(g), min = 0, max = 1)
names(weights) <- V(g)$name

ga <- Subgraph(g, weights)

subgraph <- delete.vertices(g, which(ga$population == 0))

plot(subgraph)