[BioC] Retrieving all entrez identifiers that are annotated in KEGG pathways

[Anirban [guest]]

Dear all,

Is there any way to get all entrez identifiers that are annotated with KEGG pathways? Actually I am using GOStats package in R to perform KEGG pathway enrichment analysis.. In general, for each KEGG pathway term there is a list of annotated hgnc symbols or entrez identifiers.. For all KEGG pathway terms we must have one list of entrez identifiers. I want to have that list...

What I am doing write now is as follows:
library(biomaRt)
library("GO.db")
library("KEGG.db")
library("GOstats")
library("hgu133plus2.db")
library("EMA")
library("fdrtool")
library("org.Hs.eg.db")
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") 
x <- hgu133plus2PATH
mapped_probes <- mappedkeys(x)

b<-getBM(attributes=c("hgnc_symbol"),filters="affy_hg_u133_plus_2",values=mapped_probes,mart=ensembl)

Is it the correct way to do that? 

Thanks in advance.. :)

 -- output of sessionInfo(): 

R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

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