Package: twoPhaseGAS 1.2.5
Osvaldo Espin-Garcia
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>.
Authors:
twoPhaseGAS_1.2.5.tar.gz
twoPhaseGAS_1.2.5.tar.gz(r-4.7-any)twoPhaseGAS_1.2.5.tar.gz(r-4.6-any)
twoPhaseGAS_1.2.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
twoPhaseGAS/json (API)
NEWS
| # Install 'twoPhaseGAS' in R: |
| install.packages('twoPhaseGAS', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/egosv/twophasegas/issues
Last updated from:5f85bc43c0. Checks:4 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 155 | ||
| source / vignettes | OK | 238 | ||
| linux-release-x86_64 | OK | 161 | ||
| wasm-release | OK | 123 |
Exports:DataGeneration_TPDlrtestoptimTP.GAoptimTP.LMtwoPhasetwoPhaseDesigntwoPhaseHeuristictwoPhaseSPMLtwoPhaseSPML.control
Dependencies:BHbigmemorybigmemory.sridata.tabledfoptimenrichwithkofnGAlatticeMASSMatrixnloptrRcppuuid
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| This code a function that generates a sample Y, Z, G given some initial parameters. | DataGeneration_TPD |
| Likelihood ratio test for 'twoPhaseSPML' models | lrtest lrtest.twoPhaseSPML |
| Genetic-algorithm optimal phase 2 design for a two-phase genetic association study. | optimTP.GA |
| Lagrange-multiplier optimal phase 2 design for a two-phase genetic association study. | optimTP.LM |
| Print method for 'lrtest.twoPhaseSPML' objects | print.lrtest.twoPhaseSPML |
| Print method for 'twoPhaseSPML' objects | print.twoPhaseSPML |
| Internal function to optimize over a range of maf, LD and betas. | twoPhase |
| Compute sample allocations for a two phase study design. | twoPhaseDesign |
| Select samples for phase 2 under heuristic designs. | twoPhaseHeuristic |
| Performs inference on two-phase studies data via semiparametric maximum likelihood. | twoPhaseSPML |
| Auxiliary for Controlling the EM algorithm in twoPhaseSPML. | twoPhaseSPML.control |
