coMethDMR

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see coMethDMR.

Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies

Bioconductor version: 3.15

coMethDMR identifies genomic regions associated with continuous phenotypes by optimally leverages covariations among CpGs within predefined genomic regions. Instead of testing all CpGs within a genomic region, coMethDMR carries out an additional step that selects co-methylated sub-regions first without using any outcome information. Next, coMethDMR tests association between methylation within the sub-region and continuous phenotype using a random coefficient mixed effects model, which models both variations between CpG sites within the region and differential methylation simultaneously.

Author: Fernanda Veitzman [cre], Lissette Gomez [aut], Tiago Silva [aut], Ning Lijiao [ctb], Boissel Mathilde [ctb], Lily Wang [aut], Gabriel Odom [aut]

Maintainer: Fernanda Veitzman <fveit001 at fiu.edu>

Citation (from within R, enter citation("coMethDMR")):

Installation

To install this package, start R (version "4.2") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("coMethDMR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("coMethDMR")

coMethDMR with Parallel Computing	HTML	R Script
Introduction to coMethDMR	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNAMethylation, DifferentialMethylation, Epigenetics, GenomeWideAssociation, MethylationArray, Software
Version	1.0.0
In Bioconductor since	BioC 3.15 (R-4.2) (2 years)
License	GPL-3
Depends	R (>= 4.1)
Imports	AnnotationHub, BiocParallel, bumphunter, ExperimentHub, GenomicRanges, IRanges, lmerTest, methods, stats, utils
System Requirements
URL	https://github.com/TransBioInfoLab/coMethDMR
Bug Reports	https://github.com/TransBioInfoLab/coMethDMR/issues

Suggests	BiocStyle, corrplot, knitr, rmarkdown, testthat, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	coMethDMR_1.0.0.tar.gz
Windows Binary	coMethDMR_1.0.0.zip
macOS Binary (x86_64)	coMethDMR_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/coMethDMR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/coMethDMR
Bioc Package Browser	https://code.bioconductor.org/browse/coMethDMR/
Package Short Url	https://bioconductor.org/packages/coMethDMR/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.15	Source Archive