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coMethDMR

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


Bioconductor version: Release (3.18)

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 1.6.0
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
See More
Suggests BiocStyle, corrplot, knitr, rmarkdown, testthat, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19
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Package Archives

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

Source Package coMethDMR_1.6.0.tar.gz
Windows Binary coMethDMR_1.6.0.zip (64-bit only)
macOS Binary (x86_64) coMethDMR_1.6.0.tgz
macOS Binary (arm64) coMethDMR_1.6.0.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