To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("DMRScan")

In most cases, you don't need to download the package archive at all.

DMRScan

 

Detection of Differentially Methylated Regions

Bioconductor version: Release (3.5)

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 and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("DMRScan")

Documentation

HTML R Script DMRScan.Rmd
PDF   Reference Manual
Text   NEWS

Details

biocViews Sequencing, Software, Technology, WholeGenome
Version 1.0.0
In Bioconductor since BioC 3.5 (R-3.4) (< 6 months)
License GPL-3
Depends R (>= 3.4.0)
Imports Matrix, MASS, RcppRoll, ggplot2, methods, mvtnorm, stats, parallel
LinkingTo
Suggests testthat, knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source DMRScan_1.0.0.tar.gz
Windows Binary DMRScan_1.0.0.zip
Mac OS X 10.11 (El Capitan) DMRScan_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/DMRScan
Package Short Url http://bioconductor.org/packages/DMRScan/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: