R: Two-Phase Genetic Association Study Design and Analysis with Missing Covariates by Design

# Two-Phase Genetic Association Study Design and Analysis with Missing Covariates by Design

## Documentation for package ‘twoPhaseGAS’ version 1.2.5

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

DataGeneration_TPD | This code a function that generates a sample Y, Z, G given some initial parameters.
lrtest | Likelihood ratio test for 'twoPhaseSPML' models
lrtest.twoPhaseSPML | Likelihood ratio test for 'twoPhaseSPML' models
optimTP.GA | Genetic-algorithm optimal phase 2 design for a two-phase genetic association study.
optimTP.LM | Lagrange-multiplier optimal phase 2 design for a two-phase genetic association study.
print.lrtest.twoPhaseSPML | Print method for 'lrtest.twoPhaseSPML' objects
print.twoPhaseSPML | Print method for 'twoPhaseSPML' objects
twoPhase | Internal function to optimize over a range of maf, LD and betas.
twoPhaseDesign | Compute sample allocations for a two phase study design.
twoPhaseHeuristic | Select samples for phase 2 under heuristic designs.
twoPhaseSPML | Performs inference on two-phase studies data via semiparametric maximum likelihood.
twoPhaseSPML.control | Auxiliary for Controlling the EM algorithm in twoPhaseSPML.