This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

coMethDMR

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

Bioconductor version: Release (3.17)

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 "4.3") 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

Details

biocViews DNAMethylation, DifferentialMethylation, Epigenetics, GenomeWideAssociation, MethylationArray, Software
Version 1.4.0
In Bioconductor since BioC 3.15 (R-4.2) (1.5 years)
License GPL-3
Depends R (>= 4.1)
Imports AnnotationHub, BiocParallel, bumphunter, ExperimentHub, GenomicRanges, IRanges, lmerTest, methods, stats, utils
Linking To
Suggests BiocStyle, corrplot, knitr, rmarkdown, testthat, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19
System Requirements
Enhances
URL https://github.com/TransBioInfoLab/coMethDMR
Bug Reports https://github.com/TransBioInfoLab/coMethDMR/issues
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package coMethDMR_1.4.0.tar.gz
Windows Binary coMethDMR_1.4.0.zip
macOS Binary (x86_64) coMethDMR_1.4.0.tgz
macOS Binary (arm64) coMethDMR_1.4.0.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