Python code and IPython notebooks accompanying our paper.
Specifically,
train_and_test_sets.py
- code for partitioning individuals into four sets, as shown in Figure 3aBLUP.py
- fitting the BLUP modelQTL_fitting.py
- constructing and fitting the QTL modelLMM.py
- constructing and fitting the LMM and LMM+P modelsMTLMM.py
- fitting the multi-trait LMMMRF.py
- fitting the mixed random forest
This notebook was used to produce the results for Figure 2. All models were fitted using Limix.