Compositional analysis of microbiome data using the linear decomposition model (LDM)

Abstract

Abstract Summary There are compelling reasons to test compositional hypotheses about microbiome data. We present here linear decomposition model-centered log ratio (LDM-clr), an extension of our LDM approach to allow fitting linear models to centered-log-ratio-transformed taxa count data. As LDM-clr is implemented within the existing LDM program, this extension enjoys all the features supported by LDM, including a compositional analysis of differential abundance at both the taxon and community levels, while allowing for a wide range of covariates and study designs for either association or mediation analysis. Availability and implementation LDM-clr has been added to the R package LDM, which is available on GitHub at https://github.com/yijuanhu/LDM.