*right now

On Sat, Mar 2, 2013 at 2:20 PM, Anirban [guest] <guest@bioconductor.org>wrote:

>
> 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
>
> --
> Sent via the guest posting facility at bioconductor.org.
>



-- 
______________________________________

Anirban Bhar
Department of Bioinformatics
University of Goettingen
Goettingen, Germany

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