Code for our paper: Predicting quantitative traits from genome and phenome with near perfect accuracy
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README.md

Predicting quantitative traits from genome and phenome with near perfect accuracy

Figure 2a

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 3a
  • BLUP.py - fitting the BLUP model
  • QTL_fitting.py - constructing and fitting the QTL model
  • LMM.py - constructing and fitting the LMM and LMM+P models
  • MTLMM.py - fitting the multi-trait LMM
  • MRF.py - fitting the mixed random forest

This notebook was used to produce the results for Figure 2. All models were fitted using Limix.