Package: GCPBayes 4.2.0
Yazdan Asgari
GCPBayes: Bayesian Meta-Analysis of Pleiotropic Effects Using Group Structure
Run a Gibbs sampler for a multivariate Bayesian sparse group selection model with Dirac, continuous and hierarchical spike prior for detecting pleiotropy on the traits. This package is designed for summary statistics containing estimated regression coefficients and its estimated covariance matrix. The methodology is available from: Baghfalaki, T., Sugier, P. E., Truong, T., Pettitt, A. N., Mengersen, K., & Liquet, B. (2021) <doi:10.1002/sim.8855>.
Authors:
GCPBayes_4.2.0.tar.gz
GCPBayes_4.2.0.zip(r-4.5)GCPBayes_4.2.0.zip(r-4.4)GCPBayes_4.2.0.zip(r-4.3)
GCPBayes_4.2.0.tgz(r-4.4-x86_64)GCPBayes_4.2.0.tgz(r-4.4-arm64)GCPBayes_4.2.0.tgz(r-4.3-x86_64)GCPBayes_4.2.0.tgz(r-4.3-arm64)
GCPBayes_4.2.0.tar.gz(r-4.5-noble)GCPBayes_4.2.0.tar.gz(r-4.4-noble)
GCPBayes_4.2.0.tgz(r-4.4-emscripten)GCPBayes_4.2.0.tgz(r-4.3-emscripten)
GCPBayes.pdf |GCPBayes.html✨
GCPBayes/json (API)
| # Install 'GCPBayes' in R: |
| install.packages('GCPBayes', repos = c('https://tbaghfalaki.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/tbaghfalaki/gcpbayes/issues
- DNAJC1 - Gene DNAJC1 from BCAC and Epithyr studies
- PARP2 - Gene PARP2 from CECILE study
- PARP2_summary - Summary statistics of gene PARP2 from CECILE study
- Simulated_individual - Simulated individual level data
- Simulated_individual_survival - Simulated individual level survival data
- Simulated_summary - Simulated summary statistics for K=5 traits
Last updated 8 months agofrom:631b3714a3. Checks:OK: 9. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 10 2024 |
| R-4.5-win-x86_64 | OK | Nov 10 2024 |
| R-4.5-linux-x86_64 | OK | Nov 10 2024 |
| R-4.4-win-x86_64 | OK | Nov 10 2024 |
| R-4.4-mac-x86_64 | OK | Nov 10 2024 |
| R-4.4-mac-aarch64 | OK | Nov 10 2024 |
| R-4.3-win-x86_64 | OK | Nov 10 2024 |
| R-4.3-mac-x86_64 | OK | Nov 10 2024 |
| R-4.3-mac-aarch64 | OK | Nov 10 2024 |
Exports:CSDSHSMCMCplotsummaryCSsummaryDSsummaryHS
Dependencies:abindbriocallrclicodacrayondescdiffobjdigestellipseevaluatefftwtoolsfsgdatagluegtoolsHDIntervalinvgammajsonlitelatticelifecyclemagrittrMASSmcmcOutputmcmcsemvtnormpkgbuildpkgloadplotrixpostpackpraiseprocessxpsR6RcppRcppArmadillorlangrprojrootstringistringrtestthattruncnormvctrswaldowiqidwithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Continuous Spike | CS |
| Gene DNAJC1 from BCAC and Epithyr studies | DNAJC1 |
| Dirac Spike | DS |
| Internal: e2_Monte_Carlo_EM | e2_Monte_Carlo_EM |
| GCPBayes Package | GCPBayes |
| Hierarchical Spike | HS |
| MCMC plot | MCMCplot |
| Gene PARP2 from CECILE study | PARP2 |
| Summary statistics of gene PARP2 from CECILE study | PARP2_summary |
| Simulated individual level data | Simulated_individual |
| Simulated individual level survival data | Simulated_individual_survival |
| Simulated summary statistics for K=5 traits | Simulated_summary |
| Summary function of Continuous Spike | summaryCS |
| Summary function of Dirac Spike | summaryDS |
| Summary function of Hierarchical Spike | summaryHS |
