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>.
Versions across snapshots
| Version | Repository | File | Size |
|---|---|---|---|
1.2.5 |
rolling linux/jammy R-4.5 | twoPhaseGAS_1.2.5.tar.gz |
210.3 KiB |
1.2.5 |
rolling linux/noble R-4.5 | twoPhaseGAS_1.2.5.tar.gz |
210.2 KiB |
1.2.5 |
rolling source/ R- | twoPhaseGAS_1.2.5.tar.gz |
59.0 KiB |
1.2.5 |
latest linux/jammy R-4.5 | twoPhaseGAS_1.2.5.tar.gz |
210.3 KiB |
1.2.5 |
latest linux/noble R-4.5 | twoPhaseGAS_1.2.5.tar.gz |
210.2 KiB |
1.2.5 |
latest source/ R- | twoPhaseGAS_1.2.5.tar.gz |
59.0 KiB |
1.2.5 |
2026-04-23 source/ R- | twoPhaseGAS_1.2.5.tar.gz |
0 B |