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OpTiles: an R package for adaptive tiling and methylation variability profiling.

Giorgia Migliaccio1, Lena Möbus1,2, Giusy Del Giudice1,3

  • 1Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, 33100 Tampere, Finland.

Bioinformatics (Oxford, England)
|November 9, 2025
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Summary
This summary is machine-generated.

OpTiles is a new R package for analyzing methylation data. It improves upon fixed tiling by dynamically creating windows based on CpG distribution, offering better data interpretation.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Epigenetics

Background:

  • Traditional fixed-tiling methods have limitations in analyzing targeted methylation datasets.
  • Accurate analysis of methylation variability is crucial for understanding biological processes.

Purpose of the Study:

  • To introduce OpTiles, an R package for dynamic tiling window definition in methylation analysis.
  • To address the limitations of fixed-tiling approaches in targeted methylation datasets.

Main Methods:

  • Developed an R package named OpTiles.
  • Implemented dynamic tiling window definition based on CpG distribution.
  • Integrated CpG density with intra-region methylation variability to create a reliability metric.

Main Results:

  • OpTiles dynamically defines tiling windows, overcoming fixed-tiling limitations.
  • The package provides a reliability metric for methylation data.
  • Offers extended functionality for annotating, prioritizing, and interpreting methylation data.

Conclusions:

  • OpTiles enhances the analysis of targeted methylation datasets.
  • The dynamic approach improves the reliability and interpretability of complex methylation data.
  • OpTiles is freely available as an R package with data accessible on Zenodo.