KEGG-class {AnnBuilder}R Documentation

Class "KEGG" a sub-class of pubRepo to get/process pathway and enzyme information

Description

This class is a sub-class of pubRepo with source specific functions to get/process data from KEGG {ftp://ftp.genome.ad.jp/pub/kegg/pathways} to obtain pathway and emzyme information for genes

Objects from the Class

Objects can be created by calls of the form new("KEGG", ...). A constructor (KEGG) is available and should be used to instantiate objects of this class

Slots

organism:
Object of class "character", from class "UG" a character string for the organism of concern
srcUrl:
Object of class "character", from class "UG" a character string for the url where source data are stored (ftp://ftp.genome.ad.jp/pub/kegg/pathways) at the time of coding
parser:
Object of class "character", from class "UG" not in use
baseFile:
Object of class "character", from class "UG" not in use

Extends

Class "UG", directly. Class "pubRepo", by class "UG".

Methods

findIDNPath
signature(object = "KEGG"): Finds the mappings between KEGG ids and pathway names
mapLL2ECNPName
signature(object = "KEGG"): Maps LocusLink ids to enzyme ids and pathway names

Note

This class is part of the Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics functionalities through R

Author(s)

Jianhua Zhang

References

www.genome.ad.jp/kegg/

See Also

pubRepo-class, UG-class

Examples

# The url (\url{ftp://ftp.genome.ad.jp/pub/kegg/pathways}) may change but
# was correct at the time of coding
url <-  getSrcUrl("KEGG")
kegg <- KEGG(srcUrl = url, organism = "human")
## This part takes a while to finish (due to a large number of files to
## process) and is thus commented out. Try it only if you are really
## patient
# pathNEnzyme <- mapLL2ECNPName(kegg)

[Package AnnBuilder version 1.4.21 Index]