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snpsettest
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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
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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 28 Oct. 2026.
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Complete documentation for snpsettest
Functions, R codes and Examples using
the snpsettest R package
Some associated functions: exGWAS . gene.curated.GRCh37 . gene.curated.GRCh38 . harmonize_sumstats . map_snp_to_gene . read_reference_bed . snpset_test . snpsettest-package .
Some associated R codes: RcppExports.R . davies.R . exGWAS.R . gene_gencode.R . harmonize_sumstats.R . map_snp_to_gene.R . pchisqsum.R . read_reference_bed.R . snp_match.R . snpset_test.R . snpsettest-package.R . utils.R . Full snpsettest package functions and examples
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