DMRScan
This is the released version of DMRScan; for the devel version, see DMRScan.
Detection of Differentially Methylated Regions
Bioconductor version: Release (3.23)
This package detects significant differentially methylated regions (for both qualitative and quantitative traits), using a scan statistic with underlying Poisson heuristics. The scan statistic will depend on a sequence of window sizes (# of CpGs within each window) and on a threshold for each window size. This threshold can be calculated by three different means: i) analytically using Siegmund et.al (2012) solution (preferred), ii) an important sampling as suggested by Zhang (2008), and a iii) full MCMC modeling of the data, choosing between a number of different options for modeling the dependency between each CpG.
Author: Christian M Page [aut, cre], Linda Vos [aut], Trine B Rounge [ctb, dtc], Hanne F Harbo [ths], Bettina K Andreassen [aut]
Maintainer: Christian M Page <page.ntnu at gmail.com>
citation("DMRScan")):
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")
BiocManager::install("DMRScan")
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("DMRScan")| DMR Scan Vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Sequencing, Software, Technology, WholeGenome |
| Version | 1.34.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (9.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.6.0) |
| Imports | Matrix, MASS, RcppRoll, GenomicRanges, IRanges, Seqinfo, methods, mvtnorm, stats, parallel |
| System Requirements | |
| URL | https://github.com/christpa/DMRScan |
| Bug Reports | https://github.com/christpa/DMRScan/issues |
See More
| Suggests | knitr, rmarkdown, BiocStyle, BiocManager |
| 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 | DMRScan_1.34.0.tar.gz |
| Windows Binary (x86_64) | DMRScan_1.34.0.zip |
| macOS Binary (big-sur-x86_64) | DMRScan_1.34.0.tgz |
| macOS Binary (sonoma-arm64) | DMRScan_1.34.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DMRScan |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DMRScan |
| Bioc Package Browser | https://code.bioconductor.org/browse/DMRScan/ |
| Package Short Url | https://bioconductor.org/packages/DMRScan/ |
| Package Downloads Report | Download Stats |