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arXiv · 1805.05170

FastLORS: Joint Modeling for eQTL Mapping in R

Jacob Rhyne·Eric Chi·Jung-Ying Tzeng·X. Jessie Jeng
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Abstract

Yang et al. (2013) introduced LORS, a method that jointly models the expression of genes, SNPs, and hidden factors for eQTL mapping. LORS solves a convex optimization problem and has guaranteed convergence. However, it can be computationally expensive for large datasets. In this paper we introduce Fast-LORS which uses the proximal gradient method to solve the LORS problem with significantly reduced computational burden. We apply Fast-LORS and LORS to data from the third phase of the International HapMap Project and obtain comparable results. Nevertheless, Fast-LORS shows substantial computational improvement compared to LORS.

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Jacob Rhyne, Eric Chi, Jung-Ying Tzeng, X. Jessie Jeng. 2018-05-14. FastLORS: Joint Modeling for eQTL Mapping in R. https://arxiv.org/abs/1805.05170

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