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.

Version:	1.0.4
Depends:	R (≥ 3.5.0)
Imports:	foreach, doParallel, stats, utils, ggplot2, plotly, scales, pROC
Suggests:	rmarkdown, knitr
Published:	2024-09-24
DOI:	10.32614/CRAN.package.betaclust
Author:	Koyel Majumdar [aut, cre], Romina Silva [aut], Antoinette Sabrina Perry [aut], Ronald William Watson [aut], Andrea Rau [aut], Florence Jaffrezic [aut], Thomas Brendan Murphy [aut], Isobel Claire Gormley [aut]
Maintainer:	Koyel Majumdar <koyel.majumdar at ucdconnect.ie>
License:	GPL-3
NeedsCompilation:	yes
Materials:	README NEWS
CRAN checks:	betaclust results

Documentation:

Reference manual:	betaclust.pdf
Vignettes:	betaclust: a family of beta mixture models for beta-valued DNA methylation data (source, R code)

Downloads:

Package source:	betaclust_1.0.4.tar.gz
Windows binaries:	r-devel: betaclust_1.0.4.zip, r-release: betaclust_1.0.4.zip, r-oldrel: betaclust_1.0.4.zip
macOS binaries:	r-release (arm64): betaclust_1.0.4.tgz, r-oldrel (arm64): betaclust_1.0.4.tgz, r-release (x86_64): betaclust_1.0.4.tgz, r-oldrel (x86_64): betaclust_1.0.4.tgz
Old sources:	betaclust archive

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