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.
- 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
- macOS 12.0+
- Ubuntu 20.04+
- Windows 10+
No special hardware required. Standard desktop computer with 8GB RAM sufficient for typical analyses.
Install the latest version from GitHub (typical install time: < 1 minute):
# install.packages("remotes")
remotes::install_github("stephenslab/smashr")
remotes::install_github("stephenslab/fsusieR")A brief demo with simulated methylation data can be found here.
See the pkgdown website for other examples.
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
This project is licensed under the BSD-3-Clause License - see the LICENSE file for details.
Please post issues for questions or bug reports.