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A Bayesian nonparametric analysis for zero‐inflated multivariate count data with application to microbiome study

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  • Kurtis Shuler
  • Samuel Verbanic
  • Irene A. Chen
  • Juhee Lee

Abstract

High‐throughput sequencing technology has enabled researchers to profile microbial communities from a variety of environments, but analysis of multivariate taxon count data remains challenging. We develop a Bayesian nonparametric (BNP) regression model with zero inflation to analyse multivariate count data from microbiome studies. A BNP approach flexibly models microbial associations with covariates, such as environmental factors and clinical characteristics. The model produces estimates for probability distributions which relate microbial diversity and differential abundance to covariates, and facilitates community comparisons beyond those provided by simple statistical tests. We compare the model to simpler models and popular alternatives in simulation studies, showing, in addition to these additional community‐level insights, it yields superior parameter estimates and model fit in various settings. The model's utility is demonstrated by applying it to a chronic wound microbiome data set and a Human Microbiome Project data set, where it is used to compare microbial communities present in different environments.

Suggested Citation

  • Kurtis Shuler & Samuel Verbanic & Irene A. Chen & Juhee Lee, 2021. "A Bayesian nonparametric analysis for zero‐inflated multivariate count data with application to microbiome study," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 70(4), pages 961-979, August.
    • Handle: RePEc:bla:jorssc:v:70:y:2021:i:4:p:961-979
    DOI: 10.1111/rssc.12493
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    1. De Iorio, Maria & Muller, Peter & Rosner, Gary L. & MacEachern, Steven N., 2004. "An ANOVA Model for Dependent Random Measures," Journal of the American Statistical Association, American Statistical Association, vol. 99, pages 205-215, January.
    2. Luis E. Nieto-Barajas & Peter Müller & Yuan Ji & Yiling Lu & Gordon B. Mills, 2012. "A Time-Series DDP for Functional Proteomics Profiles," Biometrics, The International Biometric Society, vol. 68(3), pages 859-868, September.
    3. Maria De Iorio & Wesley O. Johnson & Peter Müller & Gary L. Rosner, 2009. "Bayesian Nonparametric Nonproportional Hazards Survival Modeling," Biometrics, The International Biometric Society, vol. 65(3), pages 762-771, September.
    4. Gelfand, Alan E. & Kottas, Athanasios & MacEachern, Steven N., 2005. "Bayesian Nonparametric Spatial Modeling With Dirichlet Process Mixing," Journal of the American Statistical Association, American Statistical Association, vol. 100, pages 1021-1035, September.
    5. Griffin, J.E. & Steel, M.F.J., 2011. "Stick-breaking autoregressive processes," Journal of Econometrics, Elsevier, vol. 162(2), pages 383-396, June.
    6. Jialiang Mao & Yuhan Chen & Li Ma, 2020. "Bayesian Graphical Compositional Regression for Microbiome Data," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 115(530), pages 610-624, April.
    7. Russell B. Millar, 2009. "Comparison of Hierarchical Bayesian Models for Overdispersed Count Data using DIC and Bayes' Factors," Biometrics, The International Biometric Society, vol. 65(3), pages 962-969, September.
    8. David J. Spiegelhalter & Nicola G. Best & Bradley P. Carlin & Angelika Van Der Linde, 2002. "Bayesian measures of model complexity and fit," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 64(4), pages 583-639, October.
    9. Paul J McMurdie & Susan Holmes, 2014. "Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible," PLOS Computational Biology, Public Library of Science, vol. 10(4), pages 1-12, April.
    10. Jason A. Duan & Michele Guindani & Alan E. Gelfand, 2007. "Generalized Spatial Dirichlet Process Models," Biometrika, Biometrika Trust, vol. 94(4), pages 809-825.
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