DMRforPairs

DOI: 10.18129/B9.bioc.DMRforPairs    

DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles

Bioconductor version: Release (3.6)

DMRforPairs (formerly DMR2+) allows researchers to compare n>=2 unique samples with regard to their methylation profile. The (pairwise) comparison of n unique single samples distinguishes DMRforPairs from other existing pipelines as these often compare groups of samples in either single CpG locus or region based analysis. DMRforPairs defines regions of interest as genomic ranges with sufficient probes located in close proximity to each other. Probes in one region are optionally annotated to the same functional class(es). Differential methylation is evaluated by comparing the methylation values within each region between individual samples and (if the difference is sufficiently large), testing this difference formally for statistical significance.

Author: Martin Rijlaarsdam [aut, cre], Yvonne vd Zwan [aut], Lambert Dorssers [aut], Leendert Looijenga [aut]

Maintainer: Martin Rijlaarsdam <m.a.rijlaarsdam at gmail.com>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DMRforPairs")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("DMRforPairs")

 

PDF	R Script	DMRforPairs_vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, DNAMethylation, DifferentialMethylation, Microarray, ReportWriting, Software, Visualization
Version	1.14.0
In Bioconductor since	BioC 2.14 (R-3.1) (4 years)
License	GPL (>= 2)
Depends	R (>= 2.15.2), Gviz(>= 1.2.1), R2HTML (>= 2.2.1), GenomicRanges(>= 1.10.7), parallel
Imports
LinkingTo
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SystemRequirements
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URL	http://www.martinrijlaarsdam.nl http://www.erasmusmc.nl/pathologie/research/lepo/3898639/
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Package Archives

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

Source Package	DMRforPairs_1.14.0.tar.gz
Windows Binary	DMRforPairs_1.14.0.zip
Mac OS X 10.11 (El Capitan)	DMRforPairs_1.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DMRforPairs
Package Short Url	http://bioconductor.org/packages/DMRforPairs/
Package Downloads Report	Download Stats