[GenABEL-dev] Suggested RepeatABEL package

[Lars Rönnegård]

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.
-------------- next part --------------
A non-text attachment was scrubbed...
Name: StartTutorial_RepeatABEL_2015May8.pdf
Type: application/pdf
Size: 784338 bytes
Desc: StartTutorial_RepeatABEL_2015May8.pdf
URL: <http://lists.r-forge.r-project.org/pipermail/genabel-devel/attachments/20150511/760955c6/attachment-0001.pdf>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: RepeatABEL_0.1.tar.gz
Type: application/x-gzip
Size: 1902155 bytes
Desc: RepeatABEL_0.1.tar.gz
URL: <http://lists.r-forge.r-project.org/pipermail/genabel-devel/attachments/20150511/760955c6/attachment-0001.bin>