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

[Ross]

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
>
>