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
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:

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