legacy.data

A dataset containing a subset of the manifest data from the Illumina MethylationEPIC beadchip array. A subset of the complete dataset has been uploaded in the package for testing purpose. The complete dataset is available on <a href="https://github.com/koyelucd/betaclust">GitHub</a>.

datasets

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.

Koyel Majumdar

betaclust

A Family of Beta Mixture Models for Clustering Beta-Valued DNA
Methylation Data

Romina Silva

Antoinette Sabrina Perry

Ronald William Watson

Andrea Rau

Florence Jaffrezic

Thomas Brendan Murphy

Isobel Claire Gormley

legacy.data function

A data frame with 5,080 rows and 6 columns.<ul>
<li>IlmnID: The unique identifier from the Illumina CG database, i.e. the probe ID.</li>
<li>Genome_Build: The genome build referenced by the Infinium MethylationEPIC manifest.</li>
<li>CHR: The chromosome containing the CpG (Genome_Build = 37).</li>
<li>MAPINFO: The chromosomal coordinates of the CpG sites.</li>
<li>UCSC_RefGene_Name: The target gene name(s), from the UCSC database.
 Note: multiple listings of the same gene name indicate splice variants.</li>
<li>UCSC_CpG_Islands_Name: The chromosomal coordinates of the CpG Island from UCSC.</li>
</ul>

Format

A dataset containing a subset of the manifest data from the Illumina MethylationEPIC beadchip array. A subset of the complete dataset has been uploaded in the package for testing purpose. The complete dataset is available on <a href='https://github.com/koyelucd/betaclust'>GitHub</a>.

MethylationEPIC manifest data. — legacy.data

MethylationEPIC manifest data.

legacy.data: MethylationEPIC manifest data.

Description

Usage

Arguments

Format

See Also