Conditional analysis for gene- or region-based test for binary traits is now accounting for case-control imbalance 4. Since the SPA test always provides close to 0 p-values for variants with MAC = minMAFforGRM 3.Notes before running jobs FAQ can be found here More notes MetaSKAT is currently not available on CRAN.SAIGE v0.39.2 depends on the SPAtest v3.1.2./extdata/install_packages.R can be used to install the R packages.R packages: "R.utils", "Rcpp", "RcppParallel", "RcppArmadillo", "data.table", "RcppEigen", "Matrix", "methods", "BH", "optparse", "SPAtest", "SKAT","MetaSKAT".
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How to install and run SAIGE and SAIGE-GENE Install SAIGE/SAIGE-GENE List of dependencies: Willer*, Seunggeun Lee* “Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies.” Nature Genetics 50, 1335–1341 (2018) Elvestad, Brooke Wolford, Maoxuan Lin, Kristian Hveem, Hyun Min Kang, Goncalo R. Note: SAIGE-GENE accounts for case-control imbalance in gene-based tests (>= 0.35.8.5) Citation SAIGE-GENE (implemented in the SAIGE R package) performs gene- or region-based association tests (Burde, SKAT, SKAT-O) for binary traits and quantitative traits.
et.al 2017) to account for case-control imbalance.
For binary traits, SAIGE uses the saddlepoint approximation (SPA)(mhof, J. SAIGE performs single-variant association tests for binary traits and quantitative taits. Previous version is 0.44.6.1 (Updated on July 16, 2021) - SAIGE-GENE+: for group tests, collpasing ultra-rare variants with MAC 400,000). The effective sample size (Nglmm) is differently calculated than the previous versions. extdata/cmd_extractNeff.sh has the pipeline. Introduction Manuscript for SAIGE-GENE+: Current version is 0.44.6.5 (Updated on August 18, 2021) - 0.44.6.2 add extdata/extractNglmm.R to extract the effective sample size without running Step 1.
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