snpsettest: A Set-Based Association Test using GWAS Summary Statistics

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 <>.

Version: 0.1.2
Depends: R (≥ 3.1.0)
Imports: gaston, data.table, Rcpp
LinkingTo: Rcpp, RcppArmadillo
Suggests: tidyr, knitr, rmarkdown
Published: 2023-09-09
DOI: 10.32614/CRAN.package.snpsettest
Author: Jaehyun Joo [aut, cre], Blanca Himes [aut]
Maintainer: Jaehyun Joo <jaehyunjoo at>
License: GPL (≥ 3)
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_0.1.2.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): snpsettest_0.1.2.tgz, r-oldrel (arm64): snpsettest_0.1.2.tgz, r-release (x86_64): snpsettest_0.1.2.tgz, r-oldrel (x86_64): snpsettest_0.1.2.tgz
Old sources: snpsettest archive


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