To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("DMRforPairs")

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

DMRforPairs

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

Bioconductor version: Release (2.14)

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>

Citation (from within R, enter citation("DMRforPairs")):

Installation

To install this package, start R and enter:

source("http://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 1.0.2
In Bioconductor since BioC 2.14 (R-3.1)
License GPL (>= 2)
Depends R (>= 2.15.2), Gviz(>= 1.2.1), R2HTML (>= 2.2.1), GenomicRanges(>= 1.10.7), parallel
Imports
Suggests
System Requirements
URL http://www.martinrijlaarsdam.nl http://www.erasmusmc.nl/pathologie/research/lepo/3898639/
Depends On Me
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Package Archives

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

Package Source DMRforPairs_1.0.2.tar.gz
Windows Binary DMRforPairs_1.0.2.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) DMRforPairs_1.0.2.tgz
Mac OS X 10.9 (Mavericks) DMRforPairs_1.0.2.tgz
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