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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
).
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1.1.8
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Install
install.packages('MetaLonDA')
Monthly Downloads
206
Version
1.1.8
License
MIT + file LICENSE
Issues
7
Pull Requests
1
Stars
14
Forks
6
Repository
https://github.com/aametwally/MetaLonDA
Maintainer
Ahmed Metwally
Last Published
December 18th, 2019
Functions in MetaLonDA (1.1.8)
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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