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snpsettest  

A Set-Based Association Test using GWAS Summary Statistics
View on CRAN: Click here


Download and install snpsettest package within the R console
Install from CRAN:
install.packages("snpsettest")

Install from Github:
library("remotes")
install_github("cran/snpsettest")

Install by package version:
library("remotes")
install_version("snpsettest", "0.1.2")



Attach the package and use:
library("snpsettest")
Maintained by
Jaehyun Joo
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2021-03-16
Latest Update: 2023-09-09
Description:
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>.
How to cite:
Jaehyun Joo (2021). snpsettest: A Set-Based Association Test using GWAS Summary Statistics. R package version 0.1.2, https://cran.r-project.org/web/packages/snpsettest. Accessed 05 Jun. 2026.
Previous versions and publish date:
0.1.0 (2021-03-16 09:50), 0.1.1 (2022-01-18 04:40)
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Complete documentation for snpsettest
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