NEWS

---

methFuse 1.1.0 (2026-03-04)

New features

• Renamed package to methFuse to avoid name conflict in CRAN

---

New features

• Added fuse.cluster() support for BSseq and methrix objects
• Added fuse.segment() support for BSseq and methrix objects
• Unified S3 API: fuse.cluster(K0, K1) and fuse.segment(K0, K1) now supported
• fuse.cluster() now returns an hclust object

Improvements

• Improved internal argument normalization for matrix inputs
• Expanded test coverage for Bioconductor classes

Bug fixes

• Fixed incorrect handling of positional K1 arguments in S3 methods
• Fixed bug in plotting
• Now works in Windows OS

---

methFuse 1.0.0

New features

• Added plot.fuse_summary() S3 method for visualization of FUSE segmentation results.
• Segment plots now display:
  • Horizontal segment-level methylation estimates
  • Per-segment average beta values
  • Optional per-CpG methylation values overlaid as background points
• Added support for flexible segment selection when plotting (segments_to_plot).

Improvements

• Promoted package to first stable release (1.0.0).
• Improved input validation and error handling across exported functions.
• Improved S3 method registration and namespace imports.
• Improved vignette robustness and reproducibility during package checks.
• Updated documentation to reflect current plotting and summary capabilities.

Bug fixes

• Fixed S3 dispatch issues affecting plot() during vignette building.
• Fixed lazy-load and installation issues caused by partial rebuilds.
• Fixed edge cases in beta computation when counts sum to zero.
• Fixed the swapped TRUE/FALSE labels for coherent segments in fuse.summary().

---

methFuse 0.0.0.9000

Initial development release

• Implemented core FUSE pipeline:
  • fuse.cluster()
  • number.of.clusters()
  • fuse.cut.tree()
  • fuse.summary()
  • fuse.segment() (full pipeline wrapper)
• Included basic example data files for testing.
• Added introductory README and MIT license.
• Added full example workflow as an R Markdown vignette (example.Rmd).
• Enabled automatic pkgdown site deployment via GitHub Actions.