The goal of 'snpsettest' is to provide simple tools that perform set-based association tests (e.g., gene-based association tests) using GWAS (genome-wide association study) summary statistics. A set-based association test in this package is based on the statistical model described in VEGAS (versatile gene-based association study), which combines the effects of a set of SNPs accounting for linkage disequilibrium between markers. This package uses a different approach from the original VEGAS implementation to compute set-level p values more efficiently, as described in <https://github.com/HimesGroup/snpsettest/wiki/Statistical-test-in-snpsettest>.
| Version: | 0.1.1 |
| Depends: | R (≥ 3.1.0) |
| Imports: | gaston, data.table, Rcpp |
| LinkingTo: | Rcpp, RcppArmadillo |
| Suggests: | tidyr, knitr, rmarkdown |
| Published: | 2022-01-18 |
| Author: | Jaehyun Joo [aut, cre], Blanca Himes [aut] |
| Maintainer: | Jaehyun Joo <jaehyunjoo at outlook.com> |
| BugReports: | https://github.com/HimesGroup/snpsettest/issues |
| License: | GPL (≥ 3) |
| URL: | https://github.com/HimesGroup/snpsettest |
| NeedsCompilation: | yes |
| Materials: | README NEWS |
| CRAN checks: | snpsettest results |
| Reference manual: | snpsettest.pdf |
| Vignettes: |
Processing 1000 Genomes data for set-based association tests Introduction to snpsettest A set-based association test in snpsettest |
| Package source: | snpsettest_0.1.1.tar.gz |
| Windows binaries: | r-devel: snpsettest_0.1.1.zip, r-release: snpsettest_0.1.1.zip, r-oldrel: snpsettest_0.1.1.zip |
| macOS binaries: | r-release (arm64): snpsettest_0.1.1.tgz, r-oldrel (arm64): snpsettest_0.1.1.tgz, r-release (x86_64): snpsettest_0.1.1.tgz, r-oldrel (x86_64): snpsettest_0.1.1.tgz |
| Old sources: | snpsettest archive |
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