simplifyReactionNetwork {NetPathMiner} | R Documentation

## 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)

[Package NetPathMiner version 1.22.0 Index]