Package: betaclust Type: Package Title: A Family of Beta Mixture Models for Clustering Beta-Valued DNA Methylation Data Version: 1.0.3 Authors@R: c(person("Koyel", "Majumdar",email = "koyel.majumdar@ucdconnect.ie", 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) 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 NeedsCompilation: yes LazyData: true LazyDataCompression: xz RoxygenNote: 7.2.3 Suggests: rmarkdown, knitr VignetteBuilder: knitr Maintainer: Koyel Majumdar Packaged: 2023-09-29 07:56:18 UTC; koyel 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] () Repository: CRAN Date/Publication: 2023-09-29 10:20:02 UTC