DMRScan
Detection of Differentially Methylated Regions
Bioconductor version: Release (3.19)
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")
):
Installation
To install this package, start R (version "4.4") 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 | 1.26.0 |
In Bioconductor since | BioC 3.5 (R-3.4) (7.5 years) |
License | GPL-3 |
Depends | R (>= 3.6.0) |
Imports | Matrix, MASS, RcppRoll, GenomicRanges, IRanges, GenomeInfoDb, 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_1.26.0.tar.gz |
Windows Binary | DMRScan_1.26.0.zip (64-bit only) |
macOS Binary (x86_64) | DMRScan_1.26.0.tgz |
macOS Binary (arm64) | |
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 |