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DMRScan

This is the development version of DMRScan; for the stable release version, see DMRScan.

Detection of Differentially Methylated Regions


Bioconductor version: Development (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 (from within R, enter citation("DMRScan")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF
NEWS Text

Details

biocViews Sequencing, Software, Technology, WholeGenome
Version 1.25.0
In Bioconductor since BioC 3.5 (R-3.4) (7 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
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Suggests knitr, rmarkdown, BiocStyle, BiocManager
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package DMRScan_1.25.0.tar.gz
Windows Binary DMRScan_1.25.0.zip
macOS Binary (x86_64) DMRScan_1.25.0.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/
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