https://github.com/idroz/gasub
R package for extraction of active subnetworks using a global search algorithm
https://github.com/idroz/gasub
Last synced: about 2 months ago
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R package for extraction of active subnetworks using a global search algorithm
- Host: GitHub
- URL: https://github.com/idroz/gasub
- Owner: idroz
- Created: 2015-11-16T15:38:20.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2016-12-16T17:14:15.000Z (over 8 years ago)
- Last Synced: 2025-02-07T18:53:49.750Z (4 months ago)
- Language: R
- Size: 43 KB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# 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](http://julialang.org/downloads/)
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)
```