A Bayesian Binomial Regression Model with Latent Gaussian Processes for Modelling DNA Methylation

  • Aliaksandr Hubin Norwegian Computing Center, Dep.Mathematics University of Oslo
  • Geir O. Storvik Dep.Mathematics University of Oslo, Norwegian Computing Center
  • Paul E. Grini Dep. Biosciences University of Oslo
  • Melinka A. Butenko Dep. Biosciences University of Oslo

Abstract

Epigenetic observations are represented by the total number of reads from a given pool of cells and the number of methylated reads, making it reasonable to model this data by a binomial distribution. There are numerous factors that can influence the probability of success in a particular region. Moreover, there is a strong spatial (alongside the genome) dependence of these probabilities. We incorporate dependence on the covariates and the spatial dependence of the methylation probability for observations from a pool of cells by means of a binomial regression model with a latent Gaussian field and a logit link function. We apply a Bayesian approach including prior specifications on model configurations. We run a mode jumping Markov chain Monte Carlo algorithm (MJMCMC) across different choices of covariates in order to obtain the joint posterior distribution of parameters and models. This also allows finding the best set of covariates to model methylation probability within the genomic region of interest and individual marginal inclusion probabilities of the covariates.

a
Published
2020-04-13
How to Cite
Hubin, A., Storvik, G. O., Grini, P. E., & Butenko, M. A. (2020). A Bayesian Binomial Regression Model with Latent Gaussian Processes for Modelling DNA Methylation. Austrian Journal of Statistics, 49(4), 46-56. https://doi.org/10.17713/ajs.v49i4.1124
Section
Special Issue CDAM conference