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

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Documentation for package ‘twoPhaseGAS’ version 1.2.5

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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.