get.kegg.byId: Download given KEGG REACTION entry using KEGGREST package

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

View source: R/get.kegg.byId.R

Description

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

Usage

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get.kegg.byId(keggId)

Arguments

keggId

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

Value

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

Note

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

Author(s)

Byoungnam Min <[email protected]>, Byeonghyuk Park, Kyoung Heon Kim and In-Geol Choi

References

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

See Also

get.kegg.all

Examples

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# 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.