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Chen J, Zhang X. D-MANOVA: fast distance-based multivariate analysis of variance for large-scale microbiome association studies. Bioinformatics. 2021;doi: 10.1093/bioinformatics/btab498.
Chen, J., & Zhang, X. (2021). D-MANOVA: fast distance-based multivariate analysis of variance for large-scale microbiome association studies. Bioinformatics (Oxford, England), . https://doi.org/10.1093/bioinformatics/btab498
Chen, Jun, and Zhang, Xianyang. "D-MANOVA: fast distance-based multivariate analysis of variance for large-scale microbiome association studies." Bioinformatics (Oxford, England) vol. (2021). doi: https://doi.org/10.1093/bioinformatics/btab498
Chen J, Zhang X. D-MANOVA: fast distance-based multivariate analysis of variance for large-scale microbiome association studies. Bioinformatics. 2021 Jul 13; doi: 10.1093/bioinformatics/btab498. Epub 2021 Jul 13. PMID: 34255026.
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Bioinformatics. 2021 Jul 13; doi: 10.1093/bioinformatics/btab498. Epub 2021 Jul 13.

D-MANOVA: fast distance-based multivariate analysis of variance for large-scale microbiome association studies.

Bioinformatics (Oxford, England)

Jun Chen, Xianyang Zhang

Affiliations

  1. Department of Quantitative Health Sciences, Mayo Clinic, Rochester, 55901, USA.
  2. Department of Statistics, Texas A&M University, College Station, 77840, USA.

PMID: 34255026 DOI: 10.1093/bioinformatics/btab498

Abstract

SUMMARY: PERMANOVA (permutational multivariate analysis of variance based on distances) has been widely used for testing the association between the microbiome and a covariate of interest. Statistical significance is established by permutation, which is computationally intensive for large sample sizes. As large-scale microbiome studies such as American Gut Project (AGP) become increasingly popular, a computationally efficient version of PERMANOVA is much needed. To achieve this end, we derive the asymptotic distribution of the PERMANOVA pseudo-F statistic and provide analytical p-value calculation based on chi-square approximation. We show that the asymptotic p-value is close to the PERMANOVA p-value even under a moderate sample size. Moreover, it is more accurate and an order-of-magnitude faster than the permutation-free method MDMR. We demonstrated the use of our procedure D-MANOVA on the AGP dataset.

AVAILABILITY: D-MANOVA is implemented by the dmanova function in the CRAN package GUniFrac.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

© The Author(s) (2021). Published by Oxford University Press. All rights reserved. For Permissions, please email: [email protected].

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