methFuse: Functional Segmentation of the Methylome

Implements FUSE (Functional Segmentation of DNA methylation data), a data-driven method for identifying spatially coherent DNA methylation segments from whole-genome bisulfite sequencing (WGBS) count data. The method performs hierarchical clustering of CpG sites based on methylated and unmethylated read counts across multiple samples and determines the optimal number of segments using an information criterion (AIC or BIC). Resulting segments represent regions with homogeneous methylation profiles across the input cohort while allowing sample-specific methylation levels. The package provides functions for clustering, model selection, tree cutting, segment-level summarization, and visualization. Input can be supplied as count matrices or extracted directly from 'BSseq' and 'methrix' objects.

Version:	1.1.0
Imports:	stats, methods
Suggests:	bsseq, methrix, beachmat, GenomicRanges, SummarizedExperiment, DelayedArray, testthat (≥ 3.0.0), knitr, rmarkdown, graphics
Published:	2026-03-04
DOI:	10.32614/CRAN.package.methFuse (may not be active yet)
Author:	Susanna Holmström [aut, cre], Antti Hakkinen [ctb, cph]
Maintainer:	Susanna Holmström <susanna.k.holmstrom at helsinki.fi>
License:	MIT + file LICENSE
URL:	https://holmsusa.github.io/methFuse/
NeedsCompilation:	yes
Materials:	README, NEWS
CRAN checks:	methFuse results

Documentation:

Reference manual:	methFuse.html , methFuse.pdf
Vignettes:	Example workflow using FUSE (source, R code)

Downloads:

Package source:	methFuse_1.1.0.tar.gz
Windows binaries:	r-devel: not available, r-release: not available, r-oldrel: not available
macOS binaries:	r-release (arm64): methFuse_1.1.0.tgz, r-oldrel (arm64): methFuse_1.1.0.tgz, r-release (x86_64): methFuse_1.1.0.tgz, r-oldrel (x86_64): methFuse_1.1.0.tgz

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