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.