keggorthology (version 2.22.0)

getKOprobes: obtain probe set IDs associated with a KO term

Description

obtain probe set IDs associated with a KO term

Usage

getKOprobes(str, useAcc=TRUE, plat="hgu95av2", na.action=na.omit)

Arguments

str

string giving a KEGG orthology term

useAcc

logical -- use all accessible terms?

plat

platform corresponding to a bioconductor annotation package, e.g., hgu95av2.db

na.action

function for dealing with NA

Value

character vector, typically processed by na.omit

Details

Based on keggorthology read of KEGG orthology, March 2 2010. Specifically, we run wget on ftp://ftp.genome.jp/pub/kegg/brite/ko/ko00001.keg and use parsing and modeling code given in inst/keggHTML to generate a data frame respecting the hierarchy, and then keggDF2graph to construct the graph.

Looks up the requested term and gives back the unique probe set ids on the platform.

Examples

getKOtags("insulin")
es =  acc(KOgraph, "Endocrine System")
nm = names(es[[1]])
nm
esp = lapply(nm, getKOprobes)
names(esp) = nm
sapply(esp, length)