KEGGReaction-class {KEGGgraph} | R Documentation

## Class "KEGGReaction"

### Description

A class to present 'reaction' elements in KGML files

### Objects from the Class

Objects can be created by calls of the function `parseReaction`.

### Slots

`name`:

  Object of class `"character"` the KEGGID of this reaction, e.g. "rn:R02749"

`type`:

  Object of class `"character"` the type of this reaction, either 'reversible' or 'irreversible'

`substrateName`:

  Object of class `"character"`, KEGG identifier of the COMPOUND database or the GLYCAN database e.g. "cpd:C05378"

`substrateAltName`:

  Object of class `"character"` alternative name of its parent substrate element

`productName`:

  Object of class `"character"` specifies the KEGGID of the product

`productAltName`:

  Object of class `"character"` alternative name of its parent product element

### Methods

show

  `signature(object = "KEGGReaction")`: show method

getName

  `signature(object = "KEGGReaction")`: get the KEGGID of the reaction

getType

  `signature(object = "KEGGReaction")`: get the type of the reaction

getSubstrate

  `signature(object = "KEGGReaction")`: get the name of substrate

getProduct

  `signature(object = "KEGGReaction")`: get the name of product

### Author(s)

Jitao David Zhang mailto:jitao_david.zhang@roche.com

### References

KGML Document Manual http://www.genome.jp/kegg/docs/xml/

### Examples

    ## We show how to extract reactions from a 'KEGGPathway' object
    mapfile <- system.file("extdata/map00260.xml", package="KEGGgraph")

    maptest <- parseKGML(mapfile)
    mapReactions <- getReactions(maptest)

    ## More details about reaction
    reaction <- mapReactions[[1]]
    getName(reaction)
    getType(reaction)
    getSubstrate(reaction)
    getProduct(reaction)

[Package KEGGgraph version 1.50.0 Index]