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 |
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