atlasqtl is an R package for joint molecular QTL mapping in eQTL, pQTL or mQTL studies. The method is tailored to the detection of weak genetic effects, including pleiotropic effects, exerted by QTL hotspots that control multiple molecular traits. It implements a scalable Bayesian hierarchical model for variable selection in high-dimensional multi-response regression.
The model uses a horseshoe shrinkage formulation to share information across co-regulated traits, thereby flexibly adapting to the sparse nature of genetic signals. It efficiently handles thousands of genetic variants and molecular phenotypes through batch variational inference, coupled with simulated annealing to better explore complex parameter landscapes. The R package calls C++ subroutines for computational efficiency.
Reference: H. Ruffieux, A. C. Davison, J. Hager, J. Inshaw, B. Fairfax, S. Richardson, and L. Bottolo. A global-local approach for detecting hotspots in multiple response regression. The Annals of Applied Statistics, 14:905-928, 2020.
Important note: the R package depends on the GSL library which needs to be manually installed. For example on Ubuntu,
$ sudo apt-get install libgsl-devor on mac,
$ brew install gslafter having installed Homebrew.
Then, to install the package in R, run the following command:
if(!require(remotes)) install.packages("remotes")
remotes::install_github("hruffieux/atlasqtl")For a hands-on introduction to atlasqtl, check out our example repository, which contains a step-by-step illustration of the method in a QTL mapping setting.
This software uses the GPL v3 license, see LICENSE. Authors and copyright are provided in DESCRIPTION.
To report an issue, please use the atlasqtl issue tracker at github.com.