simplifyReactionNetwork

reaction.graph

The attribute to be considered as "genes". Reactions missing this annotation, will be removed.

gene.attr

If <code>FALSE</code>, only tranlocation and spontaneous reactions are removed, otherwise
all rections with no gene annotations are removed.

remove.missing.genes

An argument passed to <code><a rd-options="" href="/link/vertexDeleteReconnect?package=NetPathMiner&version=1.8.0" data-mini-rdoc="NetPathMiner::vertexDeleteReconnect">vertexDeleteReconnect</a></code>

reconnect.threshold


This function removes reaction vertices with no gene annotations as indicated by the parameter
<code>gene.attr</code>, and connect their neighbour vertices to preserve graph connectivity. This is
particularly meaningful when reactions are translocation or spontaneous reactions,
which are not catalysed by genes.


NetPathMiner is a general framework for network path
mining using genome-scale networks. It constructs networks from
KGML, SBML and BioPAX files, providing three network
representations, metabolic, reaction and gene representations.
NetPathMiner finds active paths and applies machine learning
methods to summarize found paths for easy interpretation. It
also provides static and interactive visualizations of networks
and paths to aid manual investigation.

Ahmed Mohamed

NetPathMiner

NetPathMiner for Biological Network Construction, Path Mining
and Visualization

simplifyReactionNetwork function

An argument passed to <code><a href="vertexDeleteReconnect" rd-options="">vertexDeleteReconnect</a></code>

This function removes reaction vertices with no gene annotations as indicated by the parameter
<code>gene.attr</code>, and connect their neighbour vertices to preserve graph connectivity. This is
particularly meaningful when reactions are translocation or spontaneous reactions,
which are not catalysed by genes.

simplifyReactionNetwork: Removes reactions with no gene annotations

Description

Usage

Arguments

Value

See Also

Examples