Applied Microbiome Statistics

Correlation, Association, Interaction and Composition

Yinglin Xia, Jun Sun

• Publisher: Chapman and Hall/CRC
• Year: 2024
• Print ISBN: 9780367639709
• eBook ISBN: 9781040045701
• Edition: 1
• Topic: Mathematics
• Subtopic: Probability & Statistics
• Index: Mathematics

This unique book officially defines microbiome statistics as a specific new field of statistics and addresses the statistical analysis of correlation, association, interaction, and composition in microbiome research. It also defines the study of the microbiome as a hypothesis-driven experimental science and describes two microbiome research themes and six unique characteristics of microbiome data, as well as investigating challenges for statistical analysis of microbiome data using the standard statistical methods. This book is useful for researchers of biostatistics, ecology, and data analysts.

• Presents a thorough overview of statistical methods in microbiome statistics of parametric and nonparametric correlation, association, interaction, and composition adopted from classical statistics and ecology and specifically designed for microbiome research.
• Performs step-by-step statistical analysis of correlation, association, interaction, and composition in microbiome data.
• Discusses the issues of statistical analysis of microbiome data: high dimensionality, compositionality, sparsity, overdispersion, zero-inflation, and heterogeneity.
• Investigates statistical methods on multiple comparisons and multiple hypothesis testing and applications to microbiome data.
• Introduces a series of exploratory tools to visualize composition and correlation of microbial taxa by barplot, heatmap, and correlation plot.
• Employs the Kruskal–Wallis rank-sum test to perform model selection for further multi-omics data integration.
• Offers R code and the datasets from the authors' real microbiome research and publicly available data for the analysis used.
• Remarks on the advantages and disadvantages of each of the methods used.

Table of contents

• Cover
• Half Title
• Series
• Title
• Copyright
• Dedication
• Contents
• Preface
• Acknowledgments
• About the Authors
• 1 Introduction to Microbiome Statistics
• 2 Classical Parametric Correlation
• 3 Classical Nonparametric Correlation
• 4 Composition Barplots
• 5 Composition Heatmaps
• 6 Correlation Heatmaps and Plots
• 7 Model Selection for Correlation and Association Analysis
• 8 Alpha Diversity–Based Association Analysis
• 9 Beta Diversity-Based Association Analysis
• 10 Multiple Comparisons and Multiple Hypothesis Testing
• 11 Multiple Comparisons and Multiple Hypothesis Testing in Microbiome Research
• 12 Linear Discriminant Analysis Effect Size (LEfSe)
• 13 Sparse and Compositional Methods for Inferencing Microbial Interactions
• 14 Network Construction and Comparison for Microbiome Data
• 15 Microbial Networks in Semi-Parametric Rank-Based Correlation and Partial Correlation Estimation
• References
• Index