[task list][ml] Rare Variant Analysis Task List

[akotlar]

Background: We want a rare variant analysis module because much of the variance in rare disease incidence is explained by rare mutations. We want to create rare variant methods and use those in publications to push the field of genetics forward.

Task List:

• Get underlying statistical model for Dave's simulation written out #249

• Generate realistic simulations on Dave's 2 condition simulation #250

• Convert Dave's simulation to python and match in terms of summary counts

• Write out correct statistical model for genetic correlation with Dave's agreement

• To generate data and what we should be modeling

• Test the existing models (Reduced Rank Regression, EM ZIP TADA, ML TADA, Dirichlet Process TADA) on Dave's simulations, record performance #251

• Add conversion from fitted values to relative risk and heritability #315

• Identify best performing model to use as base for multivariate version and communicate results to Dave

• Test the same models on our N>3 condition simulation and write down results

• Add Bystro Scientific Repo for experimental models that we want to publish on

• PR Adversarial model: maximizes explained, minimizes predictive ability on confounding variables. #253

  • Stretch goal: get it reviewed and in.

• Share results with Dave & ask him about Austin's N condition simulator proposal #254

[cristinaetrv]

Current task list is #391