permubiome: A Permutation Based Test for Biomarker Discovery in Microbiome Data

The permubiome R package was created to perform a permutation-based non-parametric analysis on microbiome data for biomarker discovery aims. This test executes thousands of comparisons in a pairwise manner, after a random shuffling of data into the different groups of study with a prior selection of the microbiome features with the largest variation among groups. Previous to the permutation test itself, data can be normalized according to different methods proposed to handle microbiome data ('proportions' or 'Anders'). The median-based differences between groups resulting from the multiple simulations are fitted to a normal distribution with the aim to calculate their significance. A multiple testing correction based on Benjamini-Hochberg method (fdr) is finally applied to extract the differentially presented features between groups of your dataset. LATEST UPDATES: v1.1 and olders incorporates function to parse COLUMN format; v1.2 and olders incorporates -optimize- function to maximize evaluation of features with largest inter-class variation; v1.3 and olders includes the -size.effect- function to perform estimation statistics using the bootstrap-coupled approach implemented in the 'dabestr' (>=0.3.0) R package.

Getting started

Package details

AuthorAlfonso Benitez-Paez
MaintainerAlfonso Benitez-Paez <>
Package repositoryView on CRAN
Installation Install the latest version of this package by entering the following in R:

Try the permubiome package in your browser

Any scripts or data that you put into this service are public.

permubiome documentation built on July 31, 2020, 9:08 a.m.