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
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betaclust.pdf |betaclust.html✨
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 6 months agofrom:cd0688ea7e. Checks:1 OK, 7 WARNING. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 21 2025 |
| R-4.5-win | WARNING | Feb 21 2025 |
| R-4.5-mac | WARNING | Feb 21 2025 |
| R-4.5-linux | WARNING | Feb 21 2025 |
| R-4.4-win | WARNING | Feb 21 2025 |
| R-4.4-mac | WARNING | Feb 21 2025 |
| R-4.3-win | WARNING | Feb 21 2025 |
| R-4.3-mac | WARNING | Feb 21 2025 |
Exports:AUC_WD_metricbeta_kbeta_knbeta_krbetaclustDMC_identificationecdf.betaclustem_aicem_bicem_iclthreshold
Dependencies:askpassbase64encbslibcachemclicodetoolscolorspacecpp11crosstalkcurldata.tabledigestdoParalleldplyrevaluatefansifarverfastmapfontawesomeforeachfsgenericsggplot2gluegtablehighrhtmltoolshtmlwidgetshttrisobanditeratorsjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplotlyplyrpROCpromisespurrrR6rappdirsRColorBrewerRcpprlangrmarkdownsassscalesstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunyaml
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 |
