Package: mmcmcBayes 0.2.0
Zhexuan Yang
mmcmcBayes: Multistage MCMC Method for Detecting DMRs
Implements differential methylation region (DMR) detection using a multistage Markov chain Monte Carlo (MCMC) algorithm based on the alpha-skew generalized normal (ASGN) distribution. Version 0.2.0 removes the Anderson-Darling test stage, improves computational efficiency of the core ASGN and multistage MCMC routines, and adds convenience functions for summarizing and visualizing detected DMRs. The methodology is based on Yang (2025) <https://www.proquest.com/docview/3218878972>.
Authors:
mmcmcBayes_0.2.0.tar.gz
mmcmcBayes_0.2.0.tar.gz(r-4.7-any)mmcmcBayes_0.2.0.tar.gz(r-4.6-any)
mmcmcBayes_0.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
mmcmcBayes/json (API)
| # Install 'mmcmcBayes' in R: |
| install.packages('mmcmcBayes', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/zyang1919/mmcmcbayes/issues
- cancer_demo - Cancer Methylation Demo Data
- normal_demo - Normal Methylation Demo Data
Last updated from:479faa1a26. Checks:4 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 146 | ||
| source / vignettes | OK | 174 | ||
| linux-release-x86_64 | OK | 142 | ||
| wasm-release | OK | 113 |
Exports:asgn_funccompare_dmrsmmcmcBayesplot_dmr_regionsummarize_dmrs
Dependencies:codalatticeMASSMatrixMatrixModelsmcmcMCMCpackquantregSparseMsurvival
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Fit an Alpha-Skewed Generalized Normal (ASGN) Distribution by MCMC | asgn_func |
| Cancer Methylation Demo Data | cancer_demo |
| Compare Differentially Methylated Regions (DMRs) from Two Methods | compare_dmrs |
| Multi-stage MCMC Bayesian Method for DMR Detection | mmcmcBayes |
| Normal Methylation Demo Data | normal_demo |
| Plot mean methylation profiles for a selected DMR | plot_dmr_region |
| Summarize DMR results from 'mmcmcBayes' | summarize_dmrs |