[BioC] Retrieving all entrez identifiers that are annotated in KEGG pathways
guest at bioconductor.org
Sat Mar 2 14:20:41 CET 2013
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:
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
x <- hgu133plus2PATH
mapped_probes <- mappedkeys(x)
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)
 LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
 LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
 LC_PAPER=C LC_NAME=C
 LC_ADDRESS=C LC_TELEPHONE=C
 LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
 stats graphics grDevices utils datasets methods base
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