BayesSUR: An R Package for High-Dimensional Multivariate Bayesian Variable and Covariance Selection in Linear Regression
Year: 2021
Type: article
Abstract: In molecular biology, advances in high-throughput technologies have made it possible to study complex multivariate phenotypes and their simultaneous associations with high-dimensional genomic and other omics data, a problem that can be studied with high-dimensional multi-response regression, where the response variables are potentially highly correlated. To this purpose, we recently introduced several multivariate Bayesian variable and covariance selection models, e.g., Bayesian estimation methods for sparse seemingly unrelated regression for variable and covariance selection. Several variable selection priors have been implemented in this context, in particular the hotspot detection prior for latent variable inclusion indicators, which results in sparse variable selection for associations between predictors and multiple phenotypes. We also propose an alternative, which uses a Markov random field (MRF) prior for incorporating prior knowledge about the dependence structure of the inclusion indicators. Inference of Bayesian seemingly unrelated regression (SUR) by Markov chain Monte Carlo methods is made computationally feasible by factorization of the covariance matrix amongst the response variables. In this paper we present BayesSUR, an R package, which allows the user to easily specify and run a range of different Bayesian SUR models, which have been implemented in C++ for computational efficiency. The R package allows the specification of the models in a modular way, where the user chooses the priors for variable selection and for covariance selection separately. We demonstrate the performance of sparse SUR models with the hotspot prior and spike-and-slab MRF prior on synthetic and real data sets representing eQTL or mQTL studies and in vitro anti-cancer drug screening studies as examples for typical applications.
Source: Journal of Statistical Software
Language: English
Subfield: Statistics and Probability
Field: Mathematics
Domain: Physical Sciences
Open Access status: diamond
Funders: Alan Turing Institute, National Institute for Health and Care Research, British Heart Foundation, European Commission, Universitetet i Oslo, Norges Forskningsråd, Medical Research Council, Engineering and Physical Sciences Research Council, NIHR Cambridge Biomedical Research Centre, Medisinske fakultet, Universitetet i Oslo
Awards: G1309768829, G1633672591, G2018950450, Understanding the dynamic determinants of glucose homeostasis and social capability to promote Healthy and active aging, Methods and tools for structural models integrating multiple high-throughput omics data sets in genetic epidemiology, G3855435662, G4143003329, G434337789, G444630160, The Alan Turing Institute, RESISTANCE UNDER COMBINATORIAL TREATMENT IN ER+ AND ER- BREAST CANCER., G5030582063, G5057394198, G5335488906, G5420266884, G5637460663, Unveiling the history of the Galaxy with its fossil stars, G8795210754
OpenAlex ID: W3215932503