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")Here is a quick example with simulated methylation data.
Expected output: 3 credible sets identifying causal SNPs, effect plots showing methylation changes
Basic fine-mapping analysis:
# Y: n x p matrix of molecular traits (n samples, p locations)
# X: n x J matrix of genotypes (n samples, J SNPs)
# L: maximum number of causal SNPs (default = 10)
fit <- susiF(X, Y, L = 10)
# Extract key results
fit$cs # Credible sets
fit$pip # Posterior inclusion probabilities
fit$effects # Estimated SNP effectsFor genome-wide analyses, process by genomic regions (e.g., TADs):
# Define genomic regions
regions <- define_regions(positions, window = 2e6)
# Run fSuSiE per region
results <- lapply(regions, function(r) {
susiF(X[, r$snps], Y[, r$traits], L = 20)
})See the package website for detailed tutorials and 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.