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: 0.1.0
Depends: R (≥ 3.1.0)
Imports: gaston, data.table, Rcpp
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr, rmarkdown
Published: 2021-03-16
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

Downloads:

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_0.1.0.tar.gz
Windows binaries: r-devel: snpsettest_0.1.0.zip, r-release: snpsettest_0.1.0.zip, r-oldrel: snpsettest_0.1.0.zip
macOS binaries: r-release: snpsettest_0.1.0.tgz, r-oldrel: snpsettest_0.1.0.tgz

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