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SAIGEgds

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


Bioconductor version: Release (3.18)

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>

Citation (from within R, enter citation("SAIGEgds")):

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

Details

biocViews Genetics, GenomeWideAssociation, Software, StatisticalMethod
Version 2.2.1
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License GPL-3
Depends R (>= 3.5.0), gdsfmt(>= 1.28.0), SeqArray(>= 1.36.1), Rcpp
Imports methods, stats, utils, Matrix, RcppParallel
System Requirements C++11, GNU make
URL https://github.com/AbbVie-ComputationalGenomics/SAIGEgds
See More
Suggests parallel, crayon, CompQuadForm, survey, SNPRelate, RUnit, knitr, markdown, rmarkdown, ggmanh, BiocGenerics
Linking To Rcpp, RcppArmadillo, RcppParallel (>= 5.0.0)
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package SAIGEgds_2.2.1.tar.gz
Windows Binary SAIGEgds_2.2.1.zip
macOS Binary (x86_64) SAIGEgds_2.2.1.tgz
macOS Binary (arm64) SAIGEgds_2.2.1.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 3.18 Source Archive