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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(KEGGgraph)

Attaching package: 'KEGGgraph'

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

    plot

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/KEGGgraph/KEGGReaction-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: KEGGReaction-class
> ### Title: Class "KEGGReaction"
> ### Aliases: KEGGReaction-class show,KEGGReaction-method
> ###   getName,KEGGReaction-method getSubstrate
> ###   getSubstrate,KEGGReaction-method getProduct
> ###   getProduct,KEGGReaction-method
> ### Keywords: classes
> 
> ### ** 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)
[1] "rn:R08211"
> getType(reaction)
[1] "irreversible"
> getSubstrate(reaction)
[1] "cpd:C00576"
> getProduct(reaction)
[1] "cpd:C00719"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>