simplifyReactionNetwork: Removes reactions with no gene annotations

In ahmohamed/NetPathMiner: NetPathMiner for Biological Network Construction, Path Mining and Visualization

Removes reactions with no gene annotations

Description

This function removes reaction vertices with no gene annotations as indicated by the parameter gene.attr, 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.

Usage

simplifyReactionNetwork(
  reaction.graph,
  gene.attr = "genes",
  remove.missing.genes = TRUE,
  reconnect.threshold = vcount(reaction.graph)
)

Arguments

reaction.graph	A reaction network.
gene.attr	The attribute to be considered as "genes". Reactions missing this annotation, will be removed.
remove.missing.genes	If FALSE, only tranlocation and spontaneous reactions are removed, otherwise all rections with no gene annotations are removed.
reconnect.threshold	An argument passed to vertexDeleteReconnect

Value

A simplified reaction network.

Author(s)

Ahmed Mohamed

See Also

Other Network processing methods: expandComplexes(), makeMetaboliteNetwork(), makeReactionNetwork(), reindexNetwork(), rmSmallCompounds(), vertexDeleteReconnect()

Examples

 data(ex_sbml)
 rgraph <- makeReactionNetwork(ex_sbml, simplify=FALSE)

 ## Removes all reaction nodes with no annotated genes.
 rgraph <- simplifyReactionNetwork(rgraph, remove.missing.genes=TRUE)

ahmohamed/NetPathMiner documentation built on Oct. 31, 2024, 8:01 a.m.