Implements methods for variable selection in linear regression based on the "Sum of Single Effects" (SuSiE) model, as described in Wang et al (2020) <doi:10.1101/501114>. These methods provide simple summaries, called "Credible Sets", for accurately quantifying uncertainty in which variables should be selected. The methods are motivated by genetic fine-mapping applications, and are particularly well-suited to settings where variables are highly correlated and detectable effects are sparse. The fitting algorithm, a Bayesian analogue of stepwise selection methods called "Iterative Bayesian Stepwise Selection" (IBSS), is simple and fast, allowing the SuSiE model be fit to large data sets (thousands of samples and hundreds of thousands of variables).
| Version: | 0.11.42 |
| Depends: | R (≥ 3.0.0) |
| Imports: | methods, graphics, grDevices, stats, Matrix, mixsqp, reshape, ggplot2 |
| Suggests: | testthat, microbenchmark, knitr, rmarkdown, L0Learn, genlasso |
| Published: | 2021-06-14 |
| Author: | Gao Wang [aut], Yuxin Zou [aut], Kaiqian Zhang [aut], Peter Carbonetto [aut, cre], Matthew Stephens [aut] |
| Maintainer: | Peter Carbonetto <peter.carbonetto at gmail.com> |
| BugReports: | https://github.com/stephenslab/susieR/issues |
| License: | MIT + file LICENSE |
| URL: | https://github.com/stephenslab/susieR |
| NeedsCompilation: | no |
| Citation: | susieR citation info |
| Materials: | README |
| CRAN checks: | susieR results |
| Reference manual: | susieR.pdf |
| Vignettes: |
Fine-mapping with summary statistics Fine-mapping example L0Learn initialization demo minimal example Sparse vs. dense matrix operations SuSiE with sparse matrix operations Refine SuSiE model Diagnostic for fine-mapping with summary statistics Trend filtering demo Implementation of SuSiE trend filtering |
| Package source: | susieR_0.11.42.tar.gz |
| Windows binaries: | r-devel: susieR_0.11.42.zip, r-release: susieR_0.11.42.zip, r-oldrel: susieR_0.11.42.zip |
| macOS binaries: | r-release (arm64): susieR_0.11.42.tgz, r-release (x86_64): susieR_0.11.42.tgz, r-oldrel: susieR_0.11.42.tgz |
| Old sources: | susieR archive |
| Reverse imports: | coloc |
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