SAIGEgds

DOI: 10.18129/B9.bioc.SAIGEgds  

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

Bioconductor version: Release (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 abbvie.com>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SAIGEgds")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SAIGEgds")

 

HTML	R Script	SAIGEgds Tutorial (single variant tests)
PDF		Reference Manual
Text		NEWS

Details

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
Enhances
URL	https://github.com/AbbVie-ComputationalGenomics/SAIGEgds
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	SAIGEgds_2.0.1.tar.gz
Windows Binary	SAIGEgds_2.0.1.zip (64-bit only)
macOS Binary (x86_64)	SAIGEgds_2.0.1.tgz
macOS Binary (arm64)	SAIGEgds_2.0.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SAIGEgds
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SAIGEgds
Bioc Package Browser	https://code.bioconductor.org/browse/SAIGEgds/
Package Short Url	https://bioconductor.org/packages/SAIGEgds/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive