[GenABEL-dev] Review needed for MultiABEL

[Pirastu Nicola]

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 väg 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
--
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
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/>
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-



_______________________________________________
genabel-devel mailing list
genabel-devel at lists.r-forge.r-project.org<mailto:genabel-devel at lists.r-forge.r-project.org>
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel


--
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org<mailto:lennart at karssen.org>
http://blog.karssen.org
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

_______________________________________________
genabel-devel mailing list
genabel-devel at lists.r-forge.r-project.org
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel

AVVISO DI RISERVATEZZA Informazioni riservate possono essere contenute nel messaggio o nei suoi allegati. Se non siete i destinatari indicati nel messaggio, o responsabili per la sua consegna alla persona, o se avete ricevuto il messaggio per errore, siete pregati di non trascriverlo, copiarlo o inviarlo a nessuno. In tal caso vi invitiamo a cancellare il messaggio ed i suoi allegati. Grazie. CONFIDENTIALITY NOTICE Confidential information may be contained in this message or in its attachments. If you are not the addressee indicated in this message, or responsible for message delivering to that person, or if you have received this message in error, you may not transcribe, copy or deliver this message to anyone. In that case, you should delete this message and its attachments. Thank you.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/genabel-devel/attachments/20141103/2b563e3a/attachment.html>