coMethDMR

DOI: 10.18129/B9.bioc.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>

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")

 

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

Details

biocViews	DNAMethylation, DifferentialMethylation, Epigenetics, GenomeWideAssociation, MethylationArray, Software
Version	1.0.0
In Bioconductor since	BioC 3.15 (R-4.2) (0.5 years)
License	GPL-3
Depends	R (>= 4.1)
Imports	AnnotationHub, BiocParallel, bumphunter, ExperimentHub, GenomicRanges, IRanges, lmerTest, methods, stats, utils
LinkingTo
Suggests	BiocStyle, corrplot, knitr, rmarkdown, testthat, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19
SystemRequirements
Enhances
URL	https://github.com/TransBioInfoLab/coMethDMR
BugReports	https://github.com/TransBioInfoLab/coMethDMR/issues
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_1.0.0.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
Package Short Url	https://bioconductor.org/packages/coMethDMR/
Package Downloads Report	Download Stats