DMRScan

DOI: 10.18129/B9.bioc.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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

PDF	R Script	DMRScan.Rmd
PDF		Reference Manual
Text		NEWS

Details

biocViews	Sequencing, Software, Technology, WholeGenome
Version	1.10.0
In Bioconductor since	BioC 3.5 (R-3.4) (2.5 years)
License	GPL-3
Depends	R (>= 3.4.0)
Imports	Matrix, MASS, RcppRoll, GenomicRanges, IRanges, GenomeInfoDb, 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
Links To Me
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 git@git.bioconductor.org:packages/DMRScan
Package Short Url	https://bioconductor.org/packages/DMRScan/
Package Downloads Report	Download Stats