- KNN
- Matrix Factorization
- Linear Regression
- Phenotype only
- Genotype only
- Mixed effects model
- Choosing a few SNPs to act as fixed effects in the model
- Nonlinear scaling as suggested by Fusi et al., 2014.
- A full Bayesian Mixture Model as in Dahl et al.
https://systems.genetics.ucla.edu/data/hmdp_secondset Data - Heterogenous mouse data
- Phenotype - http://mtweb.cs.ucl.ac.uk/HSMICE/PHENOTYPES/CombinedPhenotypes.txt
- Genotype - http://mtweb.cs.ucl.ac.uk/HSMICE/GENOTYPES/
Pancreatic Islet Data (too large to be uploaded on github) https://dodb.jax.org/dodb_data/downloads/8e35b16c-1d5e-4710-b813-98db2c3d4033_Attie-232_Attie_DO_Islets-GigaMUGA.zip Put it in ./DO_Islets/
- Fusi et al. 2014, Genetic Analysis of Transformed Phenotypes
- Dahl et al., 2016 A multiple-phenotype imputation method for genetic studies