DESCRIPTION

Package: SAIGE
Type: Package
Title: 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+) 
Version: 1.4.0
Date: 2024-12-11
Author: Wei Zhou, Zhangchen Zhao, Wenjian Bi, Seunggeun Lee, Cristen Willer
Maintainer: SAIGE team <saige.genetics@gmail.com> 
Description:an R package that implements the Scalable and Accurate Implementation of Generalized mixed model that uses the saddlepoint approximation (SPA)(mhof, J. P. , 1961; Kuonen, D. 1999; Dey, R. et.al 2017) and large scale optimization techniques to calibrate case-control ratios in logistic mixed model score tests (Chen, H. et al. 2016) in large PheWAS. It conducts both single-variant association tests and set-based tests for rare variants.  
License: GPL (>= 2)
Imports: Rcpp (>= 1.0.7), RcppParallel, Matrix, data.table, RcppArmadillo (>= 0.10.7.5)
LinkingTo: Rcpp, RcppArmadillo (>= 0.10.7.5), RcppParallel, data.table, SPAtest (== 3.1.2),
        RcppEigen, Matrix, methods, BH, optparse, SKAT, MetaSKAT, qlcMatrix, RhpcBLASctl, RSQLite, dplyr, lintools
Depends: R (>= 3.5.0)
SystemRequirements: GNU make
RoxygenNote: 7.1.2
NeedsCompilation: yes
Encoding: UTF-8
Packaged: 2024-12-11 EST