Package: twoPhaseGAS
Type: Package
Title: Two-Phase Genetic Association Study Design and Analysis with
        Missing Covariates by Design
Version: 1.2.5
Authors@R: c(
    person("Osvaldo", "Espin-Garcia",
           email = "oespinga@uwo.ca",
           role = c("aut", "cre")),
    person("Apostolos", "Dimitromanolakis",
           email = "apostolis@live.ca",
           role = "aut"),
    person("Radu V", "Craiu",
           email = "radu.craiu@utoronto.ca",
           role = "ths"),
    person("Shelley B", "Bull",
           email = "bull@lunenfeld.ca",
           role = "ths"))
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 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>.
License: GPL (>= 2)
URL: https://github.com/egosv/twoPhaseGAS
BugReports: https://github.com/egosv/twoPhaseGAS/issues
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)
VignetteBuilder: knitr
Encoding: UTF-8
RoxygenNote: 7.3.2
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2026-05-19 16:07:48 UTC; osvespinga
Author: Osvaldo Espin-Garcia [aut, cre],
  Apostolos Dimitromanolakis [aut],
  Radu V Craiu [ths],
  Shelley B Bull [ths]
Maintainer: Osvaldo Espin-Garcia <oespinga@uwo.ca>
Repository: CRAN
Date/Publication: 2026-05-27 10:00:02 UTC
