R: Functions to get/process pathway and enzyme data from KEGG

getKEGGIDNName {AnnBuilder}

R Documentation

Functions to get/process pathway and enzyme data from KEGG

Description

These functions extract pathway and enzyme data from KEGG ftp://ftp.genome.ad.jp/pub/kegg/pathways. The functions are used by KEGG-class.

Usage

getKEGGIDNName(srcUrl, exten = "/map\_title.tab")
getKEGGOrgName(name)
getLLPathMap(srcUrl, idNName, organism)
mapll2EC(id, srcUrl, organism, sep = "\t")
parseEC(llNEC)

Arguments

`srcUrl`	`srcUrl` a character string for the url where source data are available
`exten`	`exten` a character string for data file name as an extension
`name`	`name` a character string for the name of the organism of concern. "human", "mouse", and "rat" are the valid values for now
`organism`	`organism` same as name
`idNName`	`idNName` a named vector normally obtained obtained by using function `getKEGGIDNName`
`sep`	`sep` a character string for the separaters used to separater entries in a file
`llNEC`	`llNEC` a line of tab separated character strings with the first character string being a LocusLink id and second being the mapping enzyme (EC) names
`id`	`id` a character string for the KEGG id used for different pathway files

Details

getKEGGIDNName read the data file "map_title.tab" from KEGG to obtain the mappings between between KEGG ids and pathway names.

getKEGGOrgName takes the name for an organism and returns a short verion of the name used by KEGG for that organism.

getLLPathMap maps LocusLink ids to pathway and enzyme names for an organism using various data files from KEGG.

mapll2EC maps LocusLink ids to enzyme (EC) names for a given pathway.

parseEC extracts enzyme data from a line of tab separated character strings to map a LocusLink id to enzyme (EC) names.

Value

getKEGGIDNName returns a named vector with KEGG ids being the names and pathway names being values.
getKEGGOrgName returns a character string.
getLLPathMap returns a list of two elements named "llec" and "llpathname". Each element is a matrix with mappings between LocusLink ids to enzyme or pathway names.
mapll2EC returns a matrix with the first column being LocusLink ids and second enzyme (EC) names.
parseEC returns two elements vector with the first element being a LocusLink id and second being the mapping enzyme (EC) names.

Note

The functions are 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/

Examples

getKEGGOrgName("human")
# This group of code needs a while to finish
if(interactive()){
# Url may change but was correct at the time of coding
idNPath <- getKEGGIDNName("ftp://ftp.genome.ad.jp/pub/kegg/pathways")
temp <- getLLPathMap("ftp://ftp.genome.ad.jp/pub/kegg/pathways",
idNPath, "human")
temp <- mapll2EC("00010", "ftp://ftp.genome.ad.jp/pub/kegg/pathways",
"human", sep = "\t")
}

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