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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DMRScan")
In most cases, you don't need to download the package archive at all.
DMRScan
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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("https://bioconductor.org/biocLite.R")
biocLite("DMRScan")
Documentation
| HTML | R Script | DMRScan.Rmd |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Sequencing, Software, Technology, WholeGenome |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (0.5 years) |
| 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.
| Source Package | 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 |
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