[BioC] problem with org.Hs.egCHRLOCEND

[Marc Carlson]

Hi everyone,

If the version of the org.Hs.eg.db package is sufficiently old, then
CHRLOCEND will not be there since it was added more recently than
CHRLOC.  Please always use the most recent annotation packages.  These
things change regularly and we update them all every 6 months to try and
save you trouble caused by old information.


  Marc



James W. MacDonald wrote:
> 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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>