[BioC] can you get end position information from org.Hs.eg

[Marc Carlson]

Martin Morgan wrote:
> Hi Andrew --
>
> I guess the thread you reference is about finding entrez ids when
> chromosome locations are known, whereas you're doing something
> different. I don't think the end positions are in the org.Hs.eg
> packages.
>
> One strategy is to use biomaRt, e.g.,
>
>   
>> library(biomaRt)
>> mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl")
>> getGene(c("1", "100"), listFilters(mart)[59, 1], mart=mart)
>>     
>   entrezgene hgnc_symbol
> 1          1        A1BG
> 2        100         ADA
>                                                                                          description
> 1    Alpha-1B-glycoprotein precursor (Alpha-1-B glycoprotein). [Source:Uniprot/SWISSPROT;Acc:P04217]
> 2 Adenosine deaminase (EC 3.5.4.4) (Adenosine aminohydrolase). [Source:Uniprot/SWISSPROT;Acc:P00813]
>   chromosome_name   band strand start_position end_position ensembl_gene_id
> 1              19 q13.43     -1       63548356     63556669 ENSG00000121410
> 2              20 q13.12     -1       42681578     42713795 ENSG00000196839
>
> Martin
>
>
> "Andrew Yee" <yee at post.harvard.edu> writes:
>
>   
>> I've been exploring the org.Hs.eg package.  I can see how you can get start
>> locations of genes from org.Hs.egCHRLOC, but how do you get the end location
>> for a given gene ID?  Apologies if this is obvious.  I've already looked
>> through the info here:
>>
>> https://stat.ethz.ch/pipermail/bioconductor/2007-December/020625.html
>>
>> and don't see this explicitly addressed.
>>
>> Thanks,
>> Andrew
>>
>> 	[[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>     
>
>   

Hi Andrew,

 AFAIK none of the annotation packages has ever had the "end positions"
available.  I am still searching for more information about why we have
this tradition although I think it may be just because we have always
provided annotations that are more gene centric rather than more
transcript centric.  I take it from your request that you would like for
this information to be included as well?


     Marc