Bioconductor version: Release (3.6)
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 (from within R,
enter citation("DMRScan")
):
To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("DMRScan")
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DMRScan")
R Script | DMRScan.Rmd | |
Reference Manual | ||
Text | NEWS |
biocViews | Sequencing, Software, Technology, WholeGenome |
Version | 1.4.6 |
In Bioconductor since | BioC 3.5 (R-3.4) (1 year) |
License | GPL-3 |
Depends | R (>= 3.4.0) |
Imports | Matrix, MASS, RcppRoll, GenomicRanges, IRanges, methods, mvtnorm, stats, parallel |
LinkingTo | |
Suggests | testthat, knitr, rmarkdown |
SystemRequirements | |
Enhances | |
URL | https://github.com/christpa/DMRScan |
BugReports | https://github.com/christpa/DMRScan/issues |
Depends On Me | |
Imports Me | |
Suggests Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | DMRScan_1.4.6.tar.gz |
Windows Binary | DMRScan_1.4.6.zip |
Mac OS X 10.11 (El Capitan) | DMRScan_1.4.6.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/DMRScan |
Package Short Url | http://bioconductor.org/packages/DMRScan/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.6 | Source Archive |
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