analysis_models.md

Encore Analysis Models

savant-qt

Simple linear model

• Covariates regressed out
• Additive genotype model
• Quantitative response

savant-bin

Logistic score test

• Covariates regressed out
• Additive genotype model
• Binary response

saige-qt

Linear mixed model

• Covariates regressed out
• Additive genotype model
• Quantitative response
• Accounts for cryptic relatedness

saige-bin

Logistic mixed model

• Covariates regressed out
• Additive genotype model
• Binary response
• Accounts for cryptic relatedness
• Uses saddlepoint approximation to handle case-control imbalance