twoPhaseGAS: Two-Phase Genetic Association Study Design and Analysis with
Missing Covariates by Design
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 2 data
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>.
| Version: |
1.2.5 |
| Depends: |
R (≥ 3.5.0) |
| Imports: |
data.table, dfoptim, enrichwith, kofnGA (≥ 1.2), MASS, Matrix, nloptr, parallel, stats, utils |
| Suggests: |
gplots, knitr, rmarkdown, testthat (≥ 3.0.0) |
| Published: |
2026-05-27 |
| DOI: |
10.32614/CRAN.package.twoPhaseGAS (may not be active yet) |
| Author: |
Osvaldo Espin-Garcia [aut, cre],
Apostolos Dimitromanolakis [aut],
Radu V Craiu [ths],
Shelley B Bull [ths] |
| Maintainer: |
Osvaldo Espin-Garcia <oespinga at uwo.ca> |
| BugReports: |
https://github.com/egosv/twoPhaseGAS/issues |
| License: |
GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| URL: |
https://github.com/egosv/twoPhaseGAS |
| NeedsCompilation: |
no |
| Materials: |
README, NEWS |
| CRAN checks: |
twoPhaseGAS results |
Documentation:
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