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A web application for sample size and power calculation in case-control microbiome studies

Author:
Mattiello, Federico, Verbist, Bie, Faust, Karoline, Raes, Jeroen, Shannon, William D., Bijnens, Luc, Thas, Olivier
Source:
Bioinformatics 2016 v.32 no.13 pp. 2038-2040
ISSN:
1460-2059
Subject:
Internet, bioinformatics, case-control studies, community structure, computer software, microbiome, models, user interface
Abstract:
Summary: When designing a case-control study to investigate differences in microbial composition, it is fundamental to assess the sample sizes needed to detect an hypothesized difference with sufficient statistical power. Our application includes power calculation for (i) a recoded version of the two-sample generalized Wald test of the ‘HMP’ R-package for comparing community composition, and (ii) the Wilcoxon-Mann-Whitney test for comparing operational taxonomic unit-specific abundances between two samples (optional). The simulation-based power calculations make use of the Dirichlet-Multinomial model to describe and generate abundances. The web interface allows for easy specification of sample and effect sizes. As an illustration of our application, we compared the statistical power of the two tests, with and without stratification of samples. We observed that statistical power increases considerably when stratification is employed, meaning that less samples are needed to detect the same effect size with the same power. Availability and implementation: The web interface is written in R code using Shiny (RStudio Inc., 2016) and it is available at https://fedematt.shinyapps.io/shinyMB. The R code for the recoded generalized Wald test can be found at https://github.com/mafed/msWaldHMP. Contact: Federico.Mattiello@UGent.be
Agid:
6247198