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
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/
NeedsCompilation: yes
Packaged: 2026-02-27 14:39:28 UTC; holmsusa
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>
Repository: CRAN
Date/Publication: 2026-03-04 10:10:02 UTC
Built: R 4.4.3; x86_64-w64-mingw32; 2026-04-15 01:59:43 UTC; windows
Archs: x64
