DMRScan
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see DMRScan.
Detection of Differentially Methylated Regions
Bioconductor version: 3.9
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 "3.6") 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")| DMRScan.Rmd | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Sequencing, Software, Technology, WholeGenome |
| Version | 1.10.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (7 years) |
| License | GPL-3 |
| Depends | R (>= 3.4.0) |
| 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 | testthat, knitr, rmarkdown |
| 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_1.10.0.tar.gz |
| Windows Binary | DMRScan_1.10.0.zip |
| Mac OS X 10.11 (El Capitan) | DMRScan_1.10.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DMRScan |
| Source Repository (Developer Access) | git clone [email protected]:packages/DMRScan |
| Bioc Package Browser | https://code.bioconductor.org/browse/DMRScan/ |
| Package Short Url | https://bioconductor.org/packages/DMRScan/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |