KEGGReaction-class: Class "KEGGReaction"

In KEGGgraph: KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor

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:[e-mail]

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)

Example output

Attaching package: 'KEGGgraph'

The following object is masked from 'package:graphics':

    plot

[1] "rn:R08211"
[1] "irreversible"
[1] "cpd:C00576"
[1] "cpd:C00719"

KEGGgraph documentation built on Nov. 8, 2020, 5:42 p.m.