DOI: 10.18129/B9.bioc.DMRScan    

Detection of Differentially Methylated Regions

Bioconductor version: Release (3.6)

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 (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>

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biocViews Sequencing, Software, Technology, WholeGenome
Version 1.4.6
In Bioconductor since BioC 3.5 (R-3.4) (1 year)
License GPL-3
Depends R (>= 3.4.0)
Imports Matrix, MASS, RcppRoll, GenomicRanges, IRanges, methods, mvtnorm, stats, parallel
Suggests testthat, knitr, rmarkdown
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