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CM 229 - Phenotype Prediction / Imputation

Things we'd like to try

  • KNN
  • Matrix Factorization
  • Linear Regression
  • Phenotype only
  • Genotype only
  • Mixed effects model

Other Approaches

  • 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.

Data

https://systems.genetics.ucla.edu/data/hmdp_secondset Data - Heterogenous mouse data

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/

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