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The goal of ‘snpsettest’ is to provide simple tools that performset-based association tests (e.g., gene-based association tests) usingGWAS (genome-wide association study) summary statistics. A set-basedassociation test in this package is based on the statistical modeldescribed inVEGAS(versatilegene-basedassociationstudy), which combinesthe effects of a set of SNPs accounting for linkage disequilibriumbetween markers. This package uses a different approach from theoriginal VEGAS implementation to compute set-level p values moreefficiently, as described inhere.

To install this package,

install.packages("snpsettest")

Here is awikipage fortutorial.