[BioC] biomaRt get exon intron structure of a transcrit

[steffen at stat.Berkeley.EDU]

Hi Tao,

There isn't a difference between sequence_exon_chrom_start and
exon_chrom_start in terms of the output.  These attributes are both there
as they correspond to different 'attribute pages' which is not directly
relevant for the biomaRt API but is for the BioMart web interface. BioMart
puts limits on the number of attributes you can retrieve from different
pages/categories, this is actually zero and you have to stick within one
page.  biomaRt is a little more relaxed on this but it is still
recommended to stick to querying attributes within one page/category in
one query.

So, I would suggest using exon_chrom_start if you don't retrieve any
sequence data and use sequence_exon_chrom_start if you do retrieve
sequences in the same biomaRt query.

You can see to which page/category attributes belong to by:

> library(biomaRt)
> mart = useMart("ensembl", dataset="hsapiens_gene_ensembl")
> attrib = listAttributes(mart, showGroups=TRUE)
> head(attrib)
                 name         description     group category
1        affy_hc_g110        AFFY HC G110 EXTERNAL: Features
2       affy_hg_focus       AFFY HG FOCUS EXTERNAL: Features
3       affy_hg_u133a       AFFY HG U133A EXTERNAL: Features
4     affy_hg_u133a_2     AFFY HG U133A_2 EXTERNAL: Features
5       affy_hg_u133b       AFFY HG U133B EXTERNAL: Features
6 affy_hg_u133_plus_2 AFFY HG U133-PLUS-2 EXTERNAL: Features


Cheers,
Steffen



> Hi Jim,
>
> Thank you very much!  It works.
>
> I didn't look further down in   listAttributes(mart), so I missed those.
>
> Do you know the difference between "sequence_exon_chrom_start" vs.
> "exon_chrom_start"?
>
> ...Tao
>
>
>
>
>
> ----- Original Message ----
> From: James W. MacDonald <jmacdon at med.umich.edu>
> To: "Shi, Tao" <shidaxia at yahoo.com>
> Cc: bioconductor at stat.math.ethz.ch; johannes.rainer at tugraz.at
> Sent: Friday, November 7, 2008 11:46:30 AM
> Subject: Re: [BioC] biomaRt get exon intron structure of a transcrit
>
> Hi Tao,
>
> Does this do what you want?
>
>> getBM(c("ensembl_gene_id",
>> "sequence_exon_chrom_start","sequence_exon_chrom_end"),
>> "ensembl_gene_id", "ENSG00000204580", mart)
>    ensembl_gene_id exon_chrom_start exon_chrom_end
> 1  ENSG00000204580         30960306       30960466
> 2  ENSG00000204580         30961381       30961436
> 3  ENSG00000204580         30964444       30964570
> 4  ENSG00000204580         30964664       30964766
> 5  ENSG00000204580         30964958       30965186
>
>
>
> Best,
>
> Jim
>
> Shi, Tao wrote:
>> Hi list,
>>
>> I have the same question like this old post, but don't see any answers.
>> Wonder whether we have any answers now.
>>
>> Thanks,
>>
>> ...Tao
>>
>>
>>
>> ======================================================================================
>> https://stat.ethz.ch/pipermail/bioconductor/attachments/20070717/ef7264e5/attachment.pl
>>
>> hi,
>> i just wanted to know if it is possible to get the exon intron structure
>> of
>> a transcript from biomaRt (i.e. exon 1: start=..., stop=..., exon 2:...)
>> bests, jo
>>
>
> -- James W. MacDonald, M.S.
> Biostatistician
> Hildebrandt Lab
> 8220D MSRB III
> 1150 W. Medical Center Drive
> Ann Arbor MI 48109-5646
> 734-936-8662
>
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