[GenABEL-dev] Review needed for MultiABEL

Tue Nov 4 14:47:39 CET 2014

Hi Nicola,

Thanks for being willing to review my package. I certainly can help review yours if I have time. Which package is the one that you are waiting for review? You said “second” - did you have a first review already? 

Xia

> Date: Mon, 3 Nov 2014 12:47:44 +0000
> From: Pirastu Nicola <nicola.pirastu at burlo.trieste.it>
> To: "L.C. Karssen" <lennart at karssen.org>
> Cc: "genabel-devel at lists.r-forge.r-project.org"
> 	<genabel-devel at lists.r-forge.r-project.org>
> Subject: Re: [GenABEL-dev] Review needed for MultiABEL
> Message-ID: <0AE61AB8-BF67-4669-A84B-A92089639BEC at burlo.trieste.it>
> Content-Type: text/plain; charset="windows-1252"
> 
> Dear Lennart and Xia,
> 
> since I?m in a similar situation as Xia (I wold have a package waiting for second review),
> 
> I would propose to review Xia?s package while he could review mine if he has time.
> 
> I think this would speed up things. Also I have data which would be very good to test as multi-trait.
> 
> Anyways I would be happy to review it and test it.
> 
> Best.
> 
> Nicola
> 
> 
> Il giorno 03/nov/2014, alle ore 10:07, L.C. Karssen <lennart at karssen.org<mailto:lennart at karssen.org>> ha scritto:
> 
> Dear Xia,
> 
> On 30-10-14 23:12, Xia Shen wrote:
> Dear list,
> 
> Thanks Lennart for a fairly good introduction of me! Following this, I
> would like to inform you that a new package, MultiABEL, has been
> committed to R-Forge and successfully built. This is the first (R-only)
> version, which performs multivariate GWA analysis, i.e. testing a group
> of (co)related phenotypes against each single variant. There are also a
> replication analysis module and a simple meta-analysis module included.
> The GWA module is compatible with both GenABEL (directly typed data) and
> DatABEL (imputed data) formats of genotypes.
> 
> Thank you for contributing this package. It looks like a good addition
> to the GenABEL suite.
> 
> 
> I would kindly ask whether any of you could do a technical review of
> this new package, to ensure the coding follows GenABEL standards. You
> are certainly also welcome to contribute to future development of this
> package.
> 
> We will be happy to do the review. Any volunteers can reply to the list
> or send me a private e-mail (although we prefer the 'open' route of
> using the mailing list).
> Some time ago we set up a list of suggested questions to aid package
> reviews at
> http://genabel.r-forge.r-project.org/packageReviewGuidelines.html (of
> course, suggestions for additions, corrections, etc. are very welcome).
> 
> 
> Best regards,
> 
> Lennart.
> 
> 
> Thanks in advance!
> 
> Xia
> 
> *Xia Shen, PhD*
> shen.se<http://shen.se/> <http://shen.se/>
> 
> Department of Medical Epidemiology & Biostatistics
> Karolinska Institutet
> Nobels v?g 12A
> SE-171 77 Stockholm
> SWEDEN
> 
> MRC Human Genetics Unit
> MRC Institute of Genetics & Molecular Medicine
> University of Edinburgh
> Western General Hospital
> Crewe Road
> EH4 2XU Edinburgh
> UK
> 
> 
> Date: Thu, 30 Oct 2014 13:34:25 +0100
> From: "L.C. Karssen" <lennart at karssen.org<mailto:lennart at karssen.org> <mailto:lennart at karssen.org>>
> To: GenABEL Development list
> <genabel-devel at lists.r-forge.r-project.org<mailto:genabel-devel at lists.r-forge.r-project.org>
> <mailto:genabel-devel at lists.r-forge.r-project.org>>
> Subject: [GenABEL-dev] Introducing Xia Shen
> Message-ID: <54523051.4060502 at karssen.org<mailto:54523051.4060502 at karssen.org>
> <mailto:54523051.4060502 at karssen.org>>
> Content-Type: text/plain; charset="utf-8"
> 
> Dear list,
> 
> With this e-mail I'd like to introduce Xia Shen as a "new" member of our
> community. Some of you may know Xia from his contributions to the devel
> list or his work on GenABEL's polygenic_hglm.
> 
> In the past, both Yurii and I have worked with Xia in the past and now
> Xia has asked whether he could join the GenABEL project as well. Xia has
> a background in statistical genetics and has already worked on several R
> packages, notably bigRR [1] and hglm [2], which are both in the Suggests
> list of the GenABEL package.
> 
> Xia has been working on a new package he'd like to include in the
> GenABEL suite. I'm sure you will here more on that in the near future.
> In order to set up the package Xia has been given commit access to the
> SVN repo.
> 
> Xia, I wish you a warm welcome and look forward to your contributions.
> 
> Best,
> 
> Lennart.
> 
> 
> [1] http://cran.r-project.org/web/packages/bigRR/index.html
> [2] http://cran.r-project.org/web/packages/hglm/index.html
> --
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> L.C. Karssen
> Utrecht
> The Netherlands
> 
> lennart at karssen.org<mailto:lennart at karssen.org> <mailto:lennart at karssen.org>
> http://blog.karssen.org<http://blog.karssen.org/>
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> L.C. Karssen
> Utrecht
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> 
> lennart at karssen.org<mailto:lennart at karssen.org>
> http://blog.karssen.org
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