christpa/DMRScan: Detection of Differentially Methylated Regions

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.

Getting started

Package details

AuthorChristian M Page [aut, cre], Linda Vos [aut], Trine B Rounge [ctb, dtc], Hanne F Harbo [ths], Bettina K Andreassen [aut]
Bioconductor views Sequencing Software Technology WholeGenome
MaintainerChristian M Page <[email protected]>
LicenseGPL-3
Version1.7.4
URL https://github.com/christpa/DMRScan
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("devtools")
library(devtools)
install_github("christpa/DMRScan")
christpa/DMRScan documentation built on Nov. 7, 2018, 9:47 p.m.