Package: methFuse
Title: Functional Segmentation of the Methylome
Version: 1.1.0
Authors@R: c(
    person("Susanna", "Holmström", email = "susanna.k.holmstrom@helsinki.fi", role = c("aut", "cre"), comment = c(ORCID = "0009-0005-7542-5913")),
    person("Antti", "Hakkinen", role = c("ctb", "cph")))
Description: 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.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Imports: stats, methods
Suggests: bsseq, methrix, beachmat, GenomicRanges,
        SummarizedExperiment, DelayedArray, testthat (>= 3.0.0), knitr,
        rmarkdown, graphics
VignetteBuilder: knitr
Config/testthat/edition: 3
URL: https://holmsusa.github.io/methFuse/
Repository: https://holmsusa.r-universe.dev
Date/Publication: 2026-08-03 10:40:40 UTC
RemoteUrl: https://github.com/holmsusa/methfuse
RemoteRef: HEAD
RemoteSha: 01600cf9e322f22a79291dae05389daefa90c7ab
NeedsCompilation: yes
Packaged: 2026-10-10 13:53:42 UTC; root
Author: Susanna Holmström [aut, cre] (ORCID:
    <https://orcid.org/0009-0005-7542-5913>),
  Antti Hakkinen [ctb, cph]
Maintainer: Susanna Holmström <susanna.k.holmstrom@helsinki.fi>