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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 <https://github.com/HimesGroup/snpsettest/wiki/Statistical-test-in-snpsettest>.

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 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

Documentation:

Reference manual: snpsettest.pdf
Vignettes: Processing 1000 Genomes data for set-based association tests
Introduction to snpsettest
A set-based association test in snpsettest

Downloads:

Package source: snpsettest_0.1.2.tar.gz
Windows binaries: r-devel: snpsettest_0.1.2.zip, r-release: snpsettest_0.1.2.zip, r-oldrel: snpsettest_0.1.2.zip
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

Linking:

Please use the canonical form https://CRAN.R-project.org/package=snpsettest to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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