Metagenomics Longitudinal Differential Abundance Method
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Documentation for package ‘MetaLonDA’ version 1.1.8
Help Pages
| areaPermutation | Calculate Area Ratio (AR) of each feature's time interval for all permutations |
| curveFitting | Fit longitudinal data |
| findSigInterval | Find significant time intervals |
| intervalArea | Calculate Area Ratio (AR) of each feature's time interval |
| metalonda | Metagenomic Longitudinal Differential Abundance Analysis for one feature |
| metalondaAll | Metagenomic Longitudinal Differential Abundance Analysis for all Features |
| metalonda_test_data | Simulated data of OTU abundance for 2 phenotypes each has 5 subjects at 10 time-points |
| normalize | Normalize count matrix |
| permutation | Permute group labels |
| visualizeArea | Visualize significant time interval |
| visualizeARHistogram | Visualize Area Ratio (AR) empirical distribution |
| visualizeFeature | Visualize Longitudinal Feature |
| visualizeFeatureSpline | Visualize the feature trajectory with the fitted Splines |
| visualizeTimeIntervals | Visualize all significant time intervals for all tested features |
| visualizeVolcanoPlot | Visualize log2 fold-change and significance of each interval as volcano plot |