[R-sig-genetics] r-genetics and galaxy

[Thomas Lumley]

We have some tools that I think have been put into an R package but not sent to CRAN.  They implement the methods in http://onlinelibrary.wiley.com/resolve/doi/pdf?DOI=10.1002/gepi.20516
This has been used for data sets up to 16000 people x 1M SNPs.

I will check to see the current status of the code -- the plan is to refactor it and combine with our analysis code for a Bioconductor package.

     -thomas


On Sat, 11 Sep 2010, Ross wrote:

> Hi Brad
>
> Work on the rgenetics tools in R has more or less come to a halt - I'm
> not aware of anyone working on them and I don't think many people are
> using them although we tried hard! I think David Clayton's package
> snpMatrix can handle large datasets but it's something of a struggle
> to fit billions of genotypes efficiently into the R memory model.
>
> For me personally, a bigger problem is enabling the Faculty and
> biologists I support to work reproducibly without having to worry
> about the technical problems of hundreds of GB of data. Galaxy really
> helps with those goals so I've shifted my effort to that framework.
> The Galaxy tools do use R and BioC under the hood where they're the
> best solution - but for SNP QC, Plink seems more appropriate because
> it has the specialized reporting we needed.
>
> On Sat, Sep 11, 2010 at 6:00 AM,  <r-sig-genetics-request at r-project.org> wrote:
>
>> Message: 2
>> Date: Fri, 10 Sep 2010 16:54:46 -0700
>> From: Brad McNeney <mcneney at cs.sfu.ca>
>> To: r-sig-genetics at r-project.org
>> Subject: Re: [R-sig-genetics] R-sig-genetics Digest, Vol 8, Issue 2
>> Message-ID: <4C8AC546.6080503 at stat.sfu.ca>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> Hi Ross,
>>
>> Thanks for this.  I take it then that the QC tools you have in Galaxy
>> are not in any of the Bioconductor Genetics{Base,Design,Ped} packages?
>> If not, are there plans to update the Bioconductor packages?
>>
>> Cheers,
>>
>> Brad
>> ---
>> Brad McNeney
>> Statistics and Actuarial Science
>> Simon Fraser University
>>
>>
>
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Thomas Lumley
Professor of Biostatistics
University of Washington, Seattle