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: 1.3.1
Date: 2023-09-18
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
Depends: R (>= 3.5.0)
SystemRequirements: GNU make
RoxygenNote: 7.1.2
NeedsCompilation: yes
Encoding: UTF-8
Packaged: 2023-09-18 EST
Built: R 4.3.3; x86_64-apple-darwin13.4.0; 2024-06-05 23:34:50 UTC; unix
