| KEGG-class {AnnBuilder} | R Documentation |
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 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
organism:"character", from
class "UG" a character string for the organism of concernsrcUrl:"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 codingparser:"character", from class
"UG" not in usebaseFile:"character", from
class "UG" not in use
Class "UG", directly.
Class "pubRepo", by class "UG".
signature(object = "KEGG"): Finds the
mappings between KEGG ids and pathway namessignature(object = "KEGG"): Maps
LocusLink ids to enzyme ids and pathway namesThis class is part of the Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics functionalities through R
Jianhua Zhang
# 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)