Integrative analysis of relative abundance data and presence-absence data of the microbiome using the LDM

Abstract

SummaryWe previously developed LDM for testing hypotheses about the microbiome that performs the test at both the community level and the individual taxon level. LDM can be applied to relative abundance data and presence-absence data separately, which work well when associated taxa are abundant and rare, respectively. Here we propose an omnibus test based on LDM that allows simultaneous consideration of data at different scales, thus offering optimal power across scenarios with different association mechanisms. The omnibus test is available for the wide range of data types and analyses that are supported by LDM. Availability and ImplementationThe omnibus test 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.