Gene expression Advance Access publication August 19, 2013 iBMQ: a R/Bioconductor package for integrated Bayesian modeling of eQTL data

Motivation: Recently, mapping studies of expression quantitative loci (eQTL) (where gene expression levels are viewed as quantitative traits) have provided insight into the biology of gene regulation. Bayesian methods provide natural modeling frameworks for analyzing eQTL studies, where information shared across markers and/or genes can increase the power to detect eQTLs. Bayesian approaches tend to be computationally demanding and require specialized software. As a result, most eQTL studies use univariate methods treating each gene independently, leading to suboptimal results. Results: We present a powerful, computationally optimized and free open-source R package, iBMQ. Our package implements a joint hier-archical Bayesian model where all genes and SNPs are modeled con-currently. Model parameters are estimated using a Markov chain Monte Carlo algorithm. The free and widely used openMP parallel library speeds up computation. Using a mouse cardiac dataset, we show that iBMQ improves the detection of large trans-eQTL hotspots compared with other state-of-the-art packages for eQTL analysis. Availability: The R-package iBMQ is available from the Bioconductor Web site a