mooneymi/gsaPermute: Gene Permutation Procedure for Unbiased Gene Set Analysis

gsaPermute is an R package that can be used to create random gene sets of approximately the same composition (same number of genes with the same number of SNPs) as an a priori defined gene set (e.g. from a publicly available pathway database). As part of a gene set (pathway) analysis, this procedure can be used to calculate a null distribution of association statistics for each pathway being tested, which enables adjustment of p-values for pathway size and linkage disequilibrium (correlation between SNPs).

install.packages("remotes")
remotes::install_github("mooneymi/gsaPermute")