getKOprobes: obtain probe set IDs associated with a KO term

In keggorthology: graph support for KO, KEGG Orthology

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

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.

Value

character vector, typically processed by na.omit

Author(s)

Vince Carey <[e-mail]>

Examples

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

keggorthology documentation built on Nov. 8, 2020, 6:49 p.m.