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: 1.0.3
Depends: R (≥ 3.5.0)
Imports: foreach, doParallel, stats, utils, ggplot2, plotly, scales, pROC
Suggests: rmarkdown, knitr
Published: 2023-09-29
Author: Koyel Majumdar ORCID iD [aut, cre], Romina Silva [aut], Antoinette Sabrina Perry [aut], Ronald William Watson [aut], Andrea Rau ORCID iD [aut], Florence Jaffrezic [aut], Thomas Brendan Murphy ORCID iD [aut], Isobel Claire Gormley ORCID iD [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

Downloads:

Package source: betaclust_1.0.3.tar.gz
Windows binaries: r-devel: betaclust_1.0.3.zip, r-release: betaclust_1.0.3.zip, r-oldrel: betaclust_1.0.3.zip
macOS binaries: r-release (arm64): betaclust_1.0.3.tgz, r-oldrel (arm64): betaclust_1.0.3.tgz, r-release (x86_64): betaclust_1.0.3.tgz
Old sources: betaclust archive

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