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NN-Bayes

Scripts for our NN-Bayes paper: Tianjing Zhao, Rohan L. Fernando, and Hao Cheng. "Interpretable Artificial Neural Networks incorporating Bayesian Alphabet Models for Genome-wide Prediction and Association Studies." bioRxiv (2021). see here

NN-Bayes has a new name: "mixed effects neural networks (NN-MM)". To perform NN-Bayes in JWAS, please see documentation and latest examples. The scripts here may be invalid due to the updated NN-Bayes interface in JWAS.

Below is the description of each folder:

Folder name Description
data_simulation scripts to simulate data & simulated data
real_pig_data genotype, phenotype, map file for pig
genomic_prediction_analysis scripts for genomic prediction
gwas_analysis scripts for gwas

Other real datasets can be downloaded from: Azodi, Christina B., et al. "Benchmarking parametric and machine learning models for genomic prediction of complex traits." G3: Genes, Genomes, Genetics 9.11 (2019): 3691-3702.

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code for analyses in NN-Bayes paper

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