[R] RSNPper SNPinfo and making it handle a vector

[David Duffy]

Farrel Buchinsky <fjbuch at gmail.com> wrote:

> If I run an analysis which generates statistical tests on many SNPs I would
> naturally want to get more details on the most significant SNPs. Directly
> from within R one can get the information by loading RSNPer (from
> Bioconductor) and simply issuing a command SNPinfo(2073285). Unfortunately,
> the command cannot handle a vector and therefore only wants to do one at a
> time.
> 
> Another very useful feature for which I would like to use the same treatment
> is to use the SNPinfo as a way to get the gene information
> lapply(best.snp,function(x) try(geneDetails(SNPinfo(x))))

And Vincent Carey 525-2265 <stvjc at channing.harvard.edu> wrote:

> additionally, snpper is not particularly well maintained (builds seem
> pretty old) and i think it is going to be replaced.  so i don't plan
> to put much more effort into it until i learn more about snpper.chip.org
> durability.


You might instead look at Ensembl via the biomaRt package  -- the HapMap
Biomart interface does not (yet) implement the XML Mart interface that BiomaRt
uses (boo hiss).  These _are_ vectorized.  I have made a couple of 
wrappers specific to SNPs, which you can email me about if they sound 
useful ("snps.by.name", "snps.by.region", "annotate.snps", "maf": they 
probably need to be updated before I show them off ;)).

David Duffy


-- 
| David Duffy (MBBS PhD)                                         ,-_|\
| email: davidD at qimr.edu.au  ph: INT+61+7+3362-0217 fax: -0101  /     *
| Epidemiology Unit, Queensland Institute of Medical Research   \_,-._/
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