[BioC] problem with org.Hs.egCHRLOCEND

[James W. MacDonald]

Hi Kay,


Kay Jaja wrote:
> Does any one know where i can find org.Hs.egCHRLOCEND
> to find the end base pair position for a gene. I have downloaded 
> org.Hs.eg.db package and org.Hs.egCHRLOCEND is not there.

That is correct - the gene ends are not part of that package. You can 
use biomaRt for this.

 > library(biomaRt)
 > mart <- useMart("ensembl","hsapiens_gene_ensembl")
Checking attributes ... ok
Checking filters ... ok
 > gns <- c("CRIPAK","CAND2","STK25")
 > getBM(c("hgnc_symbol","chromosome_name", 
"start_position","end_position"), "hgnc_symbol", gns, mart)
   hgnc_symbol chromosome_name start_position end_position
1      CRIPAK               4        1378152      1379776
2       CAND2               3       12813171     12851301
3       STK25               2      242083105    242096776

Alternatively, you could use getGene(), which has a simpler interface 
but returns things you might not want.

Best,

Jim


> I have tried the following example 
>  
> Library(org.Hs.eg.db)
>  
>> glist
> [1] "CRIPAK" "CAND2"  "STK25"
>  
>> mget(eglist, org.Hs.egCHR)
> $`285464`
> [1] "4"
>  
> $`23066`
> [1] "3"
>  
> $`10494`
> [1] "2"
>  
> Find the start position:
>  > mget(eglist, org.Hs.egCHRLOC)
> $`285464`
>       4
> 1375339
>  
> $`23066`
>        3
> 12813170
>  
> $`10494`
>          2
> -242083104
>  
> And the end positions I get an error 
>  
>  
>> mget(eglist, org.Hs.egCHRLOCEND)
> Error: object "org.Hs.egCHRLOCEND" not found
> Error in mget(eglist, org.Hs.egCHRLOCEND) : 
>   error in evaluating the argument 'envir' in selecting a method for function 'mget'
>  
>  
> Thanks for your help
> 
> 
>       
> 	[[alternative HTML version deleted]]
> 
> 
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826