Efficiently controlling for case-control imbalance and sample relatedness in single-variant assoc tests (SAIGE) and controlling for sample relatedness in region-based assoc tests in large cohorts and biobanks (SAIGE-GENE)

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Documentation for package ‘SAIGE’ version 0.39

Help Pages

createSparseGRM Construct a sparse GRM for a given data set
fitNULLGLMM Fit the null logistic/linear mixed model and estimate the variance ratios by randomly selected variants
fit_SKAT_NULL Fit the null logistic mixed model and estimate the variance ratio by a set of randomly selected variants
SKATtest_usingSKATLib Run single variant score tests with SPA based on the logistic mixed model.
SPAGMMATtest Run single variant or gene- or region-based score tests with SPA based on the linear/logistic mixed model.