extract_edges

Extracts the list of directed edges (links) from a given Boolean network.

A Boolean network is a particular kind of discrete dynamical system where the variables are simple binary switches. Despite its simplicity, Boolean network modeling has been a successful method to describe the behavioral pattern of various phenomena. Applying stochastic noise to Boolean networks is a useful approach for representing the effects of various perturbing stimuli on complex systems. A number of methods have been developed to control noise effects on Boolean networks using parameters integrated into the update rules. This package provides functions to examine three such methods: Boolean network with perturbations (BNp), described by Trairatphisan et al. (2013) <doi:10.1186/1478-811X-11-46>, stochastic discrete dynamical systems (SDDS), proposed by Murrugarra et al. (2012) <doi:10.1186/1687-4153-2012-5>, and Boolean network with probabilistic edge weights (PEW), presented by Deritei et al. (2022) <doi:10.1371/journal.pcbi.1010536>. This package includes source code derived from the 'BoolNet' package, which is licensed under the Artistic License 2.0.

Mohammad Taheri-Ledari

pastboon

Simulation of Parameterized Stochastic Boolean Networks

Kaveh Kavousi

Sayed-Amir Marashi

Authors of BoolNet 

extract_edges function

<dl><dt>net</dt>
<dd>A network structure of the class <code>BooleanNetwork</code> from the <code>BoolNet</code> package.</dd>
<dt>node_names</dt>
<dd>If TRUE (default), the edges are returned by node names; otherwise, the edges are returned by node indices.</dd></dl>

Arguments

Extract edges from a Boolean network — extract_edges

<dl>

<dt>net</dt>
<dd>A network structure of the class <code>BooleanNetwork</code> from the <code>BoolNet</code> package.</dd>


<dt>node_names</dt>
<dd>If TRUE (default), the edges are returned by node names; otherwise, the edges are returned by node indices.</dd>

</dl>

extract_edges: Extract edges from a Boolean network

Description

Usage

Value

Arguments

Details

Examples