[BioC] problem with org.Hs.egCHRLOCEND

[James F. Reid]

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?

 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?

 > 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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>