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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 |
| 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 |
| Reference manual: | twoPhaseGAS.html , twoPhaseGAS.pdf |
| Vignettes: |
Introduction to twoPhaseGAS (source, R code) |
| Package source: | twoPhaseGAS_1.2.5.tar.gz |
| Windows binaries: | r-devel: twoPhaseGAS_1.2.5.zip, r-release: twoPhaseGAS_1.2.5.zip, r-oldrel: twoPhaseGAS_1.2.5.zip |
| macOS binaries: | r-release (arm64): twoPhaseGAS_1.2.5.tgz, r-oldrel (arm64): twoPhaseGAS_1.2.5.tgz, r-release (x86_64): twoPhaseGAS_1.2.5.tgz, r-oldrel (x86_64): twoPhaseGAS_1.2.5.tgz |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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