coMethDMR
This is the development version of coMethDMR; for the stable release version, see coMethDMR.
Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 1.17.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 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_1.17.0.tar.gz |
| Windows Binary (x86_64) | coMethDMR_1.17.0.zip |
| macOS Binary (big-sur-x86_64) | coMethDMR_1.17.0.tgz |
| macOS Binary (sonoma-arm64) | coMethDMR_1.17.0.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 |