DMRScan
This is thereleased version of DMRScan; for the devel version, seeDMRScan.
Detection of Differentially Methylated Regions
Bioconductor version: Release (3.22)
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 "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("DMRScan")For older versions of R, please refer to the appropriateBioconductor 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 | 1.32.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (8.5 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
FollowInstallation instructions to use this package in your R session.
| Source Package | DMRScan_1.32.0.tar.gz |
| Windows Binary (x86_64) | DMRScan_1.32.0.zip (64-bit only) |
| macOS Binary (x86_64) | DMRScan_1.32.0.tgz |
| macOS Binary (arm64) | DMRScan_1.32.0.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 |