get.kegg.byId: Download given KEGG REACTION entry using KEGGREST package
In RbioRXN: Process Rhea, KEGG, MetaCyc, Unipathway Biochemical Reaction Data

Description Usage Arguments Value Note Author(s) References See Also Examples

By implementing KEGGREST package in Bioconductor (http://www.bioconductor.org/packages/release/bioc/html/KEGGREST.html), retrieve given KEGG REACTION in data.frame() object.

1	get.kegg.byId(keggId)

keggId

single KEGG REACTION ID (R number) or multiple IDs in vector

data.frame() object where data fields include,

`ENTRY`	KEGG ID
`NAME`	Enzyme name
`DEFINITION`	Reaction equation with standard compound name
`EQUATION`	Reaction equation with KEGG ID
`ENZYME`	E.C number
`COMMENT`	Comment
`RPAIR`	KEGG RPAIR is a collection of substrate-product pairs (reactant pairs) defined for each reaction in KEGG REACTION
`PATHWAY`	KEGG PATHWAY that this reaction participates
`ORTHOLOGY`	Cross-link to KEGG ORTHOLOGY database
`REMARK`	Usually this column indicates glycan reaction-chemical reaction pair
`REFERENCE`	Publication with PMID, title, and journal name

Because "KEGGREST" package has not been deposited in CRAN, you need to manually install this package by typing:

> source("http://bioconductor.org/biocLite.R")
> biocLite("KEGGREST")

For details,
http://www.bioconductor.org/packages/release/bioc/html/KEGGREST.html

Byoungnam Min <mbnmbn00@gmail.com>, Byeonghyuk Park, Kyoung Heon Kim and In-Geol Choi

KEGGREST package: http://www.bioconductor.org/packages/release/bioc/html/KEGGREST.html
KEGG API: http://www.kegg.jp/kegg/docs/keggapi.html

get.kegg.all

# Not run:

##  get.kegg.byId("R00001")                                  # single KEGG ID
##  get.kegg.byId(c("R00001", "R00002", "R00005", "R00006")) # mutiple KEGG IDs

RbioRXN documentation built on May 29, 2017, 10:56 a.m.