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fsusieR

License

The fsusieR package implements the Sum of Single Functions (fSuSiE) method for fine-mapping molecular QTLs from spatially structured traits like DNA methylation and histone modifications. fSuSiE extends the Sum of Single Effects (SuSiE) framework using wavelet-based functional regression to capture spatial correlations in molecular traits along the genome.

System Requirements

Software Dependencies

  • R (≥ 3.5.0)
  • Required R packages: wavethresh (≥ 4.6.8), ashr (≥ 2.2-47), mixsqp (≥ 0.3-43), matrixStats (≥ 0.62.0), smashr
  • Optional: susieR and mvsusieR for comparation with fSuSiE

Operating Systems

  • macOS 12.0+
  • Ubuntu 20.04+
  • Windows 10+

Hardware

No special hardware required. Standard desktop computer with 8GB RAM sufficient for typical analyses.

Installation

Install the latest version from GitHub (typical install time: < 1 minute):

# install.packages("remotes")
remotes::install_github("stephenslab/smashr")
remotes::install_github("stephenslab/fsusieR")

Demo

A brief demo with simulated methylation data can be found here.

See the pkgdown website for other examples.

Citing this work

If you use fsusieR in your work, please cite:

Denault, W.R.P., Sun, H., Carbonetto, P., Li, A., De Jager, L.P., Bennett, D, The Alzheimer’s Disease Functional Genomics Consortium, Wang, G. & Stephens, M. (2025). fSuSiE enables fine-mapping of QTLs from genome-scale molecular profiles. bioRxiv DOI: 10.1101/2025.08.17.670732

License

This project is licensed under the BSD-3-Clause License - see the LICENSE file for details.

Support

Please post issues for questions or bug reports.