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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 here.
To install this package,
install.packages("snpsettest")Here is a wiki page for tutorial.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.