TY - JOUR
AU - Li,, Hongzhe
AB - Abstract Quantitative comparison of microbial composition from different populations is a fundamental task in various microbiome studies. We consider two-sample testing for microbial compositional data by leveraging the phylogenetic tree information. Motivated by existing phylogenetic distances, we take a minimum-cost flow perspective to study such testing problems. We first show that multivariate analysis of variance with permutation using phylogenetic distances, one of the most commonly used methods in practice, is essentially a sum-of-squares type of test and has better power for dense alternatives. However, empirical evidence from real datasets suggests that the phylogenetic microbial composition difference between two populations is usually sparse. Motivated by this observation, we propose a new maximum type test, detector of active flow on a tree, and investigate its properties. We show that the proposed method is particularly powerful against sparse phylogenetic composition difference and enjoys certain optimality. The practical merit of the proposed method is demonstrated by simulation studies and an application to a human intestinal biopsy microbiome dataset on patients with ulcerative colitis. This content is only available as a PDF. © 2020 Biometrika Trust This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)
TI - Hypothesis testing for phylogenetic composition: a minimum-cost flow perspective
JF - Biometrika
DO - 10.1093/biomet/asaa061
DA - 2020-02-01
UR - https://www.deepdyve.com/lp/oxford-university-press/hypothesis-testing-for-phylogenetic-composition-a-minimum-cost-flow-hd0xWIuSwi
DP - DeepDyve
ER -