Package: betaclust
Type: Package
Title: A Family of Beta Mixture Models for Clustering Beta-Valued DNA
        Methylation Data
Version: 1.0.5
Authors@R: c(person("Koyel", "Majumdar",email = "koyelmajumdar.phdresearch@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-4692-9002")),
    person("Romina","Silva",email="romina.silva@ucdconnect.ie",role="aut"),
        person("Antoinette Sabrina","Perry",email="antoinette.perry@ucd.ie",role="aut"),
        person("Ronald William","Watson",email="william.watson@ucd.ie",role="aut"),
        person("Andrea","Rau",email="andrea.rau@inrae.fr",role="aut",comment = c(ORCID = "0000-0001-6469-488X")),
        person("Florence","Jaffrezic",email="florence.jaffrezic@inrae.fr",role="aut"),
        person("Thomas Brendan", "Murphy",email = "brendan.murphy@ucd.ie", role = c("aut"), comment = c(ORCID = "0000-0002-5668-7046")),
    person("Isobel Claire", "Gormley",email = "claire.gormley@ucd.ie", role = c("aut"), comment = c(ORCID = "0000-0001-7713-681X")))
Description: 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.
License: GPL-3
Depends: R (>= 3.5.0)
Imports: foreach, doParallel, stats, utils, ggplot2, plotly, scales,
        pROC
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
RoxygenNote: 7.3.2
Suggests: rmarkdown, knitr
VignetteBuilder: knitr
Maintainer: Koyel Majumdar <koyelmajumdar.phdresearch@gmail.com>
NeedsCompilation: no
Packaged: 2025-09-18 17:06:56 UTC; koyel
Author: Koyel Majumdar [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-4692-9002>),
  Romina Silva [aut],
  Antoinette Sabrina Perry [aut],
  Ronald William Watson [aut],
  Andrea Rau [aut] (ORCID: <https://orcid.org/0000-0001-6469-488X>),
  Florence Jaffrezic [aut],
  Thomas Brendan Murphy [aut] (ORCID:
    <https://orcid.org/0000-0002-5668-7046>),
  Isobel Claire Gormley [aut] (ORCID:
    <https://orcid.org/0000-0001-7713-681X>)
Repository: CRAN
Date/Publication: 2025-09-19 07:40:02 UTC
Built: R 4.6.0; ; 2026-04-30 07:53:44 UTC; unix
