CRAN/E | permubiome

permubiome

A Permutation Based Test for Biomarker Discovery in Microbiome Data

Installation

About

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. Current v1.3.2 fixed bug with "Class" recognition and updated 'dabestr' functions.

Key Metrics

Version 1.3.2
Published 2023-10-16 359 days ago
Needs compilation? no
License GPL-3
CRAN checks permubiome results

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Maintainer

Maintainer

Alfonso Benitez-Paez

Authors

Alfonso Benitez-Paez

Material

Reference manual
Package source

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

permubiome archive

Imports

ggplot2
rlang
dabestr
gridExtra
Matrix
dplyr