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>.


Reference manual

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0.1.1 by Jaehyun Joo, 6 days ago


Report a bug at https://github.com/HimesGroup/snpsettest/issues

Browse source code at https://github.com/cran/snpsettest

Authors: Jaehyun Joo [aut, cre] , Blanca Himes [aut]

Documentation:   PDF Manual  

GPL (>= 3) license

Imports gaston, data.table, Rcpp

Suggests tidyr, knitr, rmarkdown

Linking to Rcpp, RcppArmadillo

See at CRAN