coMethDMR
This package is for version 3.17 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: 3.17
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("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 | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, DifferentialMethylation, Epigenetics, GenomeWideAssociation, MethylationArray, Software |
| Version | 1.4.0 |
| 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 |
| 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_1.4.0.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 |
| Old Source Packages for BioC 3.17 | Source Archive |