Hi James,

Thanks a lot..

Best regards,

Anirban
On Sat, Mar 2, 2013 at 7:41 PM, James W. MacDonald <jmacdon@uw.edu> wrote:

> Hi Anirban,
>
> > library(hgu133plus2.db)
> > x <- select(hgu133plus2.db, Lkeys(hgu133plus2PATH), c("ENTREZID","PATH"))
> Warning message:
> In .generateExtraRows(tab, keys, jointype) :
>   'select' resulted in 1:many mapping between keys and return rows
> > head(x)
>     PROBEID ENTREZID  PATH
> 1 1007_s_at      780 <NA>
> 2   1053_at     5982 03030
> 3   1053_at     5982 03420
>
> > egids <- unique(x$ENTREZID[!is.na(x$**PATH)])
> > length(egids)
> [1] 5498
>
>
> Best,
>
> Jim
>
>
>
>
>
> On 3/2/2013 8:20 AM, Anirban [guest] 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.
>>
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>>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>


-- 
______________________________________

Anirban Bhar
Department of Bioinformatics
University of Goettingen
Goettingen, Germany

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