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twoPhaseGAS  

Two-Phase Genetic Association Study Design and Analysis with Missing Covariates by Design
View on CRAN: Click here


Download and install twoPhaseGAS package within the R console
Install from CRAN:
install.packages("twoPhaseGAS")

Install from Github:
library("remotes")
install_github("cran/twoPhaseGAS")

Install by package version:
library("remotes")
install_version("twoPhaseGAS", "1.2.5")



Attach the package and use:
library("twoPhaseGAS")
Maintained by
Osvaldo Espin-Garcia
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2026-05-27
Latest Update: 2026-05-27
Description:
Provides functionality for designing and analysing two-phase genetic association studies. Phase 1 data usually come from genome-wide association study (GWAS) results and we assume phase 2data will be part of a targeted genome sequencing or fine-mapping study. At design stage, the package assists in selecting a subset of individuals that will be sequenced for phase 2 via alternative approaches, including a flexible genetic algorithm (GA) for near-optimal designs. Once phase 2 data have been collected, the package implements methods to analyse phase 1 and phase 2 data together using semi-parametric regression models via the expectation-maximization (EM) algorithm. For more details see Espin-Garcia, Craiu and Bull (2018) <doi:10.1002/gepi.22099> and Espin-Garcia, Craiu and Bull (2021) <doi:10.1002/sim.9211>.
How to cite:
Osvaldo Espin-Garcia (2026). twoPhaseGAS: Two-Phase Genetic Association Study Design and Analysis with Missing Covariates by Design. R package version 1.2.5, https://cran.r-project.org/web/packages/twoPhaseGAS. Accessed 24 Oct. 2026.
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