[GenABEL-dev] Suggested RepeatABEL package

[L.C. Karssen]

Dear Lars,

First of all, sorry for the delay in answering your e-mail.

Thank you for submitting your RepeatABEL package to the list. I will put
it on my "to review" list and hope to have a look at it later next week.
In the mean time I hope one of the other GenABEL developers steps
forward and reviews your package as well.


Best regards,

Lennart.

On 11-05-15 12:53, Lars Rönnegård wrote:
> 
> Dear GenABEL developers, I attach the source code for a package I
> have developed, and I would like it to be considered for the GenABEL
> suite of packages in the future.
> 
> The RepeatABEL package connects multiple phenotypic observations in
> an R data frame with the genotype information on the individuals
> given in a GenABEL object. One can perform GWAS for data having
> repeated observations on related individuals. The hglm package is
> used for variance component estimation and there are also other
> functionalities including spatial modelling.
> 
> The code was applied in Husby et al. (2015: Genome-wide association
> mapping in a wild avian population identifies a link between genetic
> and phenotypic variation in a life history trait. Proceedings of the
> Royal Society B: Biological Sciences, 282(1806), 20150156.) and now
> we have put the code together in a package and evaluated the method
> using simulations (with Eryn McFarlane and others, manuscript in
> preparation). I therefore believe it is ready for evaluation by the
> GenABEL developers.
> 
> The package will be especially useful for GWAS in wildlife studies
> where there are large fluctuations in phenotypes between years, and
> these temporal effects are important to include in the model. I have
> a manuscript together with my co-authors that we plan to submit
> within the near future with a focus on GWAS in natural populations.
> But it should also be quite useful for most studies (including human)
> having repeated observations since it should be rather user friendly
> considering the alternatives, eg regression using average phenotypes,
> some GRAMMAR type of approach.
> 
> Any suggested improvements are appreciated.
> 
> Looking forward to your response, Lars Rönnegård
> 
> Professor of Statistics Dalarna University, Sweden 
> www.larsronnegard.se
> 
> 
> PS The name "RepeatABEL" was suggested by Xia Shen, which I very much
> appreciate.
> 
> 
> 
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> 
-- 
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L.C. Karssen
Utrecht
The Netherlands

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

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