[BioC] can not link the genomic positions queried and their specific annotation, when getting genomic variants annotated by biomaRt package

[Mao Jianfeng]

Steve,

Sorry for the troubles to you. And, thanks so much for you kindness to me.

I do not want to send questions to you directly. Very sorry. I have no
reason to do that. Sorry.

I can not to hire any bioinformatician. Aslo, I can not hire myself,
because I have no money and funding.

Though I have not got any training on bioinformatics, in fact I got
much from R/bioconductor and also their mailinglist. This is the only
way for me to pursuit my research interest.

Sorry and Thanks again to you.

Best regards,

Jian-Feng,





2011/2/9 Steve Lianoglou <mailinglist.honeypot at gmail.com>:
> Hi Mao,
>
> Please include the bioc mailing list in the cc that you get the best
> help possible.
>
> On Tue, Feb 8, 2011 at 1:10 PM, Mao Jianfeng <jianfeng.mao at gmail.com> wrote:
>> No.
>>
>> All your code just return several lines of various attributes (like
>> defined in biomart), but it is none sense for me. I need my SNPs and
>> various attributes they correspond to.
>>
>> I do not know if biomaRt can do that.
>>
>> Please read the simple example followed:
>>
>> I have SNPs like this:
>> # SNPs,chr,start,end
>> SNP_1,1,43,43
>> SNP_2,2,56,56
>>
>> I would want to have annotations like this:
>> ############################################
>> #the chr, start, end here are for my SNPs not for the gos.
>> ############################################
>> # SNPs,chr,start,end,go_term
>> SNP_1,1,43,43,go_1
>> SNP_1,1,43,43,go_3
>> SNP_2,2,56,56,go_100
>> SNP_2,2,56,56,go_1000
>>
>> Not, just
>> # chr,start,end,go_term
>> 1,43,43,go_1
>> 1,43,43,go_3
>> 2,56,56,go_100
>> 2,56,56,go_1000
>
> So ... is the problem that the code I gave you previously gives you
> "gene-level" annotations, and you want to reassociate them to snps, or
> what?
>
> Search the bioconductor archives for "snp annotation" and you'll find
> a few things:
>
> http://thread.gmane.org/gmane.science.biology.informatics.conductor/32759/focus=32846
>
> And this might help too:
>
> http://thread.gmane.org/gmane.science.biology.informatics.conductor/32267
>
> If your problem is what I understand it to be, those threads may give
> you a hint as to how you can use some tools in bioconductor to solve
> your situation, even though they aren't answers to your *direct*
> question.
>
> Hope that helps,
>
> -steve
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>



-- 
Jian-Feng, Mao

the Institute of Botany,
Chinese Academy of Botany,