A faster lmm for GWAS. GPU support coming soon.
NOTICE: this software is under active development. YMMV.
Faster_lmm_d is a lightweight linear mixed-model solver for use in genome-wide association studies (GWAS). The original is similar to FaST-LMM (an algorithm by Lippert et al.) and that code base can be found here. Prof. Karl Broman wrote a comparison with his R/lmmlite. Faster_lmm_d and pylmm are part of the Genenetwork2 project. faster_lmm_d can parse data in R/qtl2 format as input.
In order to use the gem, you also need faster_lmm_d tool installed.
Install the gem by executing:
$ gem install bio-faster_lmm_d
bio-faster_lmm_d --geno geno_file --pheno pheno_file --ctrl ctrl_file
After checking out the repo, run bin/setup to install dependencies. Then, run rake test to run the tests. You can also run bin/console for an interactive prompt that will allow you to experiment.
Bug reports and pull requests are welcome on GitHub at https://github.com/prasunanand/bio-faster_lmm_d. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the Contributor Covenant code of conduct.
This software is distributed under the GPL3 license.
Copyright © 2016, 2017, Prasun Anand and Pjotr Prins