[BioC] problem with org.Hs.egCHRLOCEND

[James W. MacDonald]

Hi James,

James F. Reid wrote:
> Hi James and Kay,
> 
> I can see org.Hs.egCHRLOCEND in both the current release version 2.2.11 
> and the devel release 2.3.0.
> In which version has this been removed or does not appear?

Good call - I do remember that this was supposed to be added, but 
neglected to look to see if it had happened.

> 
>  From ucsc I get that the following RefSeq genes coordinates:
> CRIPAK at chr4:1375340-1379782 - (NM_175918) cysteine-rich PAK1 inhibitor
> CAND2 at chr3:12813171-12851301 - (NM_012298) TBP-interacting protein
> STK25 at chr2:242083105-242096707 - (NM_006374) serine/threonine kinase 25
> 
> the starting positions obtained via CHRLOC all have an offset of -1 but 
> not the ending positions (CHRLOCEND), do you know why that is?

http://genome.ucsc.edu/FAQ/FAQtracks#tracks1

Best,

Jim


> 
>  > library("org.Hs.eg.db")
>  > org.Hs.egCHRLOCEND
> CHRLOCEND map for Human (object of class "AnnDbMap")
>  > glist <- c("CRIPAK", "CAND2", "STK25")
>  > eglist <- unlist(mget(glist, org.Hs.egSYMBOL2EG))
>  > eglist
>   CRIPAK    CAND2    STK25
> "285464"  "23066"  "10494"
>  > mget(eglist, org.Hs.egCHRLOC)
> $`285464`
>       4
> 1375339
> 
> $`23066`
>        3
> 12813170
> 
> $`10494`
>          2
> -242083104
> 
>  > mget(eglist, org.Hs.egCHRLOCEND)
> $`285464`
>       4
> 1379782
> 
> $`23066`
>        3
> 12851301
> 
> $`10494`
>          2
> -242096707
> 
>  > sessionInfo()
> R version 2.9.0 (2009-04-17)
> x86_64-redhat-linux-gnu
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C 
> 
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] org.Hs.eg.db_2.2.11 RSQLite_0.7-1       DBI_0.2-4
> [4] AnnotationDbi_1.6.0 Biobase_2.4.1
> 
> Best,
> J.
> 
> 
> James W. MacDonald wrote:
>> 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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>>>
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>>
> 
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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