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

Abstract

SummaryThere are compelling reasons to test compositional hypotheses about microbiome data. We present here LDM-clr, an extension of our linear decomposition model (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, it 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 ImplementationLDM-clr has been added to the R package LDM, which is available on GitHub at https://github.com/yijuanhu/LDM. Contactyijuan.hu@emory.edu Supplementary informationSupplementary data are available at Bioinformatics online.