Bayesian model search and multilevel inference for SNP association studies

DOI10.1214/09-AOAS322zbMath1202.62166arXiv0908.1144OpenAlexW1988591324WikidataQ34416368 ScholiaQ34416368MaRDI QIDQ614148

Joellen M. Schildkraut, Melanie A. Wilson, Scott C. Schmidler, Merlise A. Clyde, Edwin S. jun. Iversen

Publication date: 27 December 2010

Published in: The Annals of Applied Statistics (Search for Journal in Brave)

Full work available at URL: https://arxiv.org/abs/0908.1144

zbMATH Keywords

Bayes factormodel uncertaintyvariable selectionAICBICBayesian model averaginglassoevolutionary Monte Carlosingle nucleotide polymorphismgenetic modelsfalse discovery

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Bayesian inference (62F15) Medical applications (general) (92C50)

Related Items

Prior distributions for objective Bayesian analysis, A Bayesian graphical model for genome-wide association studies (GWAS), Bayesian model search and multilevel inference for SNP association studies, Bayesian Genome- and Epigenome-Wide Association Studies with Gene Level Dependence, A new flexible Bayesian hypothesis test for multivariate data, Simultaneous SNP identification in association studies with missing data, Joint specification of model space and parameter space prior distributions, Bayesian model selection in complex linear systems, as illustrated in genetic association studies, A Bayesian nonparametric multiple testing procedure for comparing several treatments against a control, Subjective Bayesian testing using calibrated prior probabilities

Uses Software

• R
• CRAN
• lasso2
• MISA
• LogicReg

Cites Work

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• Bayes and empirical-Bayes multiplicity adjustment in the variable-selection problem
• Bayesian model search and multilevel inference for SNP association studies
• Bayesian model averaging: A tutorial. (with comments and a rejoinder).
• Inference from iterative simulation using multiple sequences
• Model uncertainty
• Empirical Bayes vs. fully Bayes variable selection
• Identification of SNP interactions using logic regression
• A Direct Approach to False Discovery Rates
• Bayes Factors
• Correlation and Large-Scale Simultaneous Significance Testing