DESCRIPTION

Package: atlasqtl
Type: Package
Title: Flexible sparse regression for hierarchically-related responses using annealed variational inference
Version: 0.1.5
Date: 2024-01-02
Authors@R: c(
    person("Helene", "Ruffieux", email = "helene.ruffieux@mrc-bsu.cam.ac.uk",
            role = c("aut", "cre")),
    person("Sylvia", "Richardson", email = "sylvia.richardson@mrc-bsu.cam.ac.uk",
            role = c("aut")),
    person("Leonardo", "Bottolo", email = "lb664@cam.ac.uk",
            role = c("aut")))
Description: Flexible sparse regression for variable selection in large 
    predictor and response settings, based on a series of hierarchically-related 
    spike-and-slab submodels. The model is also tailored to the detection of 
    hotspots, namely, predictors associated with multiple responses, which it 
    represents using a global-local horseshoe specification. Inference uses 
    closed-form variational updates coupled with a simulated annealing algorithm 
    to enhance exploration of highly multimodal spaces. This software allows 
    joint inference at large scale, e.g., for molecular quantitative trait locus 
    (QTL) studies, where the hotspots are genetic variants regulating several 
    molecular traits simultaneously. See 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.
Depends:
    R (>= 3.2.0)
License: GPL (>= 3) | file LICENSE
LazyData: TRUE
Imports:
    gsl (>= 1.9-10.3),
    LaplacesDemon (>= 16.1.1),
    parallel,
    PowerTOST (>= 1.4-6),
    Rcpp (>= 0.12.9),
    RcppEigen (>= 0.3.2.9.0)
RoxygenNote: 7.2.3
Suggests: testthat
LinkingTo: Rcpp, RcppEigen
Encoding: UTF-8