Joint Analysis of Genotype and Group-Specific Variability Using a Novel Score Test Approach to Map Expression Quantitative Trait Loci (eQTL)

Implements a novel score test that measures 1) the overall shift in the gene expression due to genotype (additive genetic effect), and 2) group-specific changes in gene expression due to genotype (interaction effect) in a mixed-effects model framework.

This is an R-package to implement a novel score test method to map group-specific expression quantitative trait loci (eQTL) that tests for the additive genotypic effect and variability among tissues in a mixed effects model framework. This approach implicitly assumes that the effect of a SNP on gene expression could be in different directions in different tissues. The newest version appliesa closed-form expression of our model and speeds up the computations using templated C++ linear algebra library, Armadillo.

This package is free software, you can redistribute it and/or modify it under the terms of the GNU General Public License.The GNU General Public License does not permit this software to be redistributed in proprietary programs. We are providing no guarantees with this software.


Reference manual

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3.0.1 by Chaitanya Acharya, 3 years ago

Browse source code at

Authors: Chaitanya R. Acharya and Andrew S. Allen

Documentation:   PDF Manual  

GPL-2 license

Depends on Rcpp, plyr, lme4, reshape2

Linking to RcppArmadillo, Rcpp, RcppProgress

See at CRAN