lookbackjh / pwd

a code for Pointwise Entropy Distributions for a Group Characteristic in High-dimensional and Sparse Microbiome Compositions

A code for Pointwise Entropy Distributions for a Group Characteristic in High-dimensional and Sparse Microbiome Compositions

How to use

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run main.py to try various simulation, you can change various conditions based on your preference.

You can test two types of simulation

1. Same-ratio(k) Sensitivity Analysis

set parser.args.task as 1 and by varying the level of same_ratio and number of features(num_features) you can check the p-value and its standard deviation after repeated permutation.

2. Sparse-level Sensitivity Analysis

set parser.args.task as 0 you are able to generate each group with various sparse ratio difference level, and you can check the p-value and its standard deviation.

Tutorial

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from Example folder, you can see examples of synthetic data generation and meta analysis of them, , origianl version of permutation with phylum-level microbiome, and plots of ordered pointwise entropy. Instructions are detailed in Jupyter notebook.