Package: betaclust 1.0.4
betaclust: A Family of Beta Mixture Models for Clustering Beta-Valued DNA Methylation Data
A family of novel beta mixture models (BMMs) has been developed by Majumdar et al. (2022) <doi:10.48550/arXiv.2211.01938> to appositely model the beta-valued cytosine-guanine dinucleotide (CpG) sites, to objectively identify methylation state thresholds and to identify the differentially methylated CpG (DMC) sites using a model-based clustering approach. The family of beta mixture models employs different parameter constraints applicable to different study settings. The EM algorithm is used for parameter estimation, with a novel approximation during the M-step providing tractability and ensuring computational feasibility.
Authors:
betaclust_1.0.4.tar.gz
betaclust_1.0.4.zip(r-4.7)betaclust_1.0.4.zip(r-4.6)betaclust_1.0.4.zip(r-4.5)
betaclust_1.0.4.tgz(r-4.6-any)betaclust_1.0.4.tgz(r-4.5-any)
betaclust_1.0.4.tar.gz(r-4.7-any)betaclust_1.0.4.tar.gz(r-4.6-any)
betaclust_1.0.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
betaclust/json (API)
NEWS
| # Install 'betaclust' in R: |
| install.packages('betaclust', repos = c('https://koyelucd.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/koyelucd/betaclust/issues
- legacy.data - MethylationEPIC manifest data.
- pca.methylation.data - DNA methylation data from patients with prostate cancer
Last updated from:cd0688ea7e. Checks:7 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | WARNING | 164 | ||
| source / vignettes | OK | 251 | ||
| linux-release-x86_64 | WARNING | 160 | ||
| macos-release-arm64 | WARNING | 112 | ||
| macos-oldrel-arm64 | WARNING | 118 | ||
| windows-devel | WARNING | 119 | ||
| windows-release | WARNING | 113 | ||
| windows-oldrel | WARNING | 118 | ||
| wasm-release | OK | 136 |
Exports:AUC_WD_metricbeta_kbeta_knbeta_krbetaclustDMC_identificationecdf.betaclustem_aicem_bicem_iclthreshold
Dependencies:askpassbase64encbslibcachemclicodetoolscpp11crosstalkcurldata.tabledigestdoParalleldplyrevaluatefarverfastmapfontawesomeforeachfsgenericsggplot2gluegtablehighrhtmltoolshtmlwidgetshttrisobanditeratorsjquerylibjsonliteknitrlabelinglaterlazyevallifecyclemagrittrmemoisemimeopensslotelpillarpkgconfigplotlypROCpromisespurrrR6rappdirsRColorBrewerRcpprlangrmarkdownS7sassscalesstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| AUC and WD function | AUC_WD_metric |
| Fit the K.. model | beta_k |
| Fit the KN. model | beta_kn |
| Fit the K.R Model | beta_kr |
| The betaclust wrapper function | betaclust |
| The DMC identification function | DMC_identification |
| The empirical cumulative distribution function plot | ecdf.betaclust |
| Akaike Information Criterion | em_aic |
| Bayesian Information Criterion | em_bic |
| Integrated Complete-data Likelihood (ICL) Criterion | em_icl |
| MethylationEPIC manifest data. | legacy.data |
| DNA methylation data from patients with prostate cancer | pca.methylation.data |
| Plots for visualizing the betaclust class object | plot.betaclust |
| Summarizing the beta mixture model fits | summary.betaclust |
| Thresholds under the K.. and the KN. models | threshold |
