Two-Phase Genetic Association Study Design and Analysis with Missing Covariates by Design.
twoPhaseGAS
Two-Phase Genetic Association Study design and analysis with missing covariates by design
Description
Provides functionality for selecting and analyzing individuals in two-phase genetic association studies. Phase 1 data usually come from GWAS results and we assume phase 2 genetic data will be part of a targeted genome sequencing/fine-mapping study. The package assists in selecting a subset of individuals that will be sequenced for phase 2. Once phase 2 data have been collected, the package implements methods to analyze phase 1 and 2 data together using semi-parametric regression models.
Installation
You can install the current version of twoPhaseGAS from GitHub using (devtools required):
devtools::install_github("egosv/twoPhaseGAS", ref="main")