Learn R Programming

MetaLonDA (version 1.1.8)

Metagenomics Longitudinal Differential Abundance Method

Description

Identify time intervals of differentially abundant metagenomic features in longitudinal studies (Metwally AA, et al., Microbiome, 2018 ).

Copy Link

Version

Install

install.packages('MetaLonDA')

Monthly Downloads

32

Version

1.1.8

License

MIT + file LICENSE

Issues

7

Pull Requests

1

Stars

16

Forks

7

Maintainer

Ahmed Metwally

Last Published

December 18th, 2019

Functions in MetaLonDA (1.1.8)

metalonda_test_data

Simulated data of OTU abundance for 2 phenotypes each has 5 subjects at 10 time-points
permutation

Permute group labels
curveFitting

Fit longitudinal data
areaPermutation

Calculate Area Ratio (AR) of each feature's time interval for all permutations
visualizeArea

Visualize significant time interval
visualizeARHistogram

Visualize Area Ratio (AR) empirical distribution
visualizeFeature

Visualize Longitudinal Feature
findSigInterval

Find significant time intervals
metalonda

Metagenomic Longitudinal Differential Abundance Analysis for one feature
metalondaAll

Metagenomic Longitudinal Differential Abundance Analysis for all Features
visualizeVolcanoPlot

Visualize log2 fold-change and significance of each interval as volcano plot
intervalArea

Calculate Area Ratio (AR) of each feature's time interval
visualizeFeatureSpline

Visualize the feature trajectory with the fitted Splines
visualizeTimeIntervals

Visualize all significant time intervals for all tested features
normalize

Normalize count matrix