DOI: 10.18129/B9.bioc.SAIGEgds  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see SAIGEgds.

Scalable Implementation of Generalized mixed models using GDS files in Phenome-Wide Association Studies

Bioconductor version: 3.17

Scalable implementation of generalized mixed models with highly optimized C++ implementation and integration with Genomic Data Structure (GDS) files. It is designed for single variant tests and set-based aggregate tests in large-scale Phenome-wide Association Studies (PheWAS) with millions of variants and samples, controlling for sample structure and case-control imbalance. The implementation is based on the SAIGE R package (v0.45, Zhou et al. 2018 and Zhou et al. 2020), and it is extended to include the state-of-the-art ACAT-O set-based tests. Benchmarks show that SAIGEgds is significantly faster than the SAIGE R package.

Author: Xiuwen Zheng [aut, cre] , Wei Zhou [ctb] (the original author of the SAIGE R package), J. Wade Davis [ctb]

Maintainer: Xiuwen Zheng <xiuwen.zheng at>

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biocViews Genetics, GenomeWideAssociation, Software, StatisticalMethod
Version 2.0.1
In Bioconductor since BioC 3.10 (R-3.6) (4 years)
License GPL-3
Depends R (>= 3.5.0), gdsfmt(>= 1.28.0), SeqArray(>= 1.36.1), Rcpp
Imports methods, stats, utils, Matrix, RcppParallel
LinkingTo Rcpp, RcppArmadillo, RcppParallel (>= 5.0.0)
Suggests parallel, crayon, CompQuadForm, survey, SNPRelate, RUnit, knitr, markdown, rmarkdown, ggmanh, BiocGenerics
SystemRequirements C++11, GNU make
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