Hi Martin,

Thanks for that. I tried your code and got:

--------------------------------------------
>   egid = revmap(org.Hs.egSYMBOL)[["WNT16"]]  
>   org.Hs.egCHRLOC[[egid]]

        7         7 
120752656 120756325 

>   org.Hs.egCHRLOCEND[[egid]]

        7         7 
120768394 120768394
--------------------------------------------

However, if I go to NCBI site (http://www.ncbi.nlm.nih.gov/sites/entrez) and search for 'WNT16', I get the following information for WNT16:



Chromosome: 7;Location: 7q31
Annotation: Chromosome 7, NC_000007.13 (120965421..120981158)


Why is there a discrepancy between the values returned from bioconductor (UCSC?) and NCBI? Is there anything I can do that will get me a match with the NCBI location numbers?


thanks!



 





Hi Tim --

One suggestion is to use the org.Hs.eg.db package. The 'eg' means that
the information is keyed off Entrez ids, so you need to map your SYMBOL
to EG

  egid = revmap(org.Hs.egSYMBOL)[["WNT16"]]

and then retrieve location information

  org.Hs.egCHRLOC[[egid]]
  org.Hs.egCHRLOCEND[[egid]]

for many symbols, symids, one might

  egids = mappedLkeys(revmap(org.Hs.egSYMBOL)[symids])
  as.list(org.Hs.egCHRLOC[egids])

etc. Some book-keeping might be needed to ensure correct symid -> egid
-> CHRLOC mapping

Martin

Tim Smith wrote:

> Hi,
> 
> I wanted the exact base pair locations for several genes (e.g. wnt16 in the human wnt pathway). Which bioconductor package should I use?
> 
> thanks!
> 
> 
> 


      
	[[alternative HTML version deleted]]

