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 namesJianhua Zhang
## Not run: # 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") pathNEnzyme <- mapLL2ECNPName(kegg) ## End(Not run)