SAIGEgds

This is the development version of SAIGEgds; for the stable release version, see SAIGEgds.

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

Bioconductor version: Development (3.21)

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] (ORCID: ), 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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Genetics, GenomeWideAssociation, Software, StatisticalMethod
Version	2.7.0
In Bioconductor since	BioC 3.10 (R-3.6) (5 years)
License	GPL-3
Depends	R (>= 3.5.0), gdsfmt(>= 1.28.0), SeqArray(>= 1.43.7), Rcpp
Imports	methods, stats, utils, Matrix, RcppParallel, CompQuadForm, survey
System Requirements	C++11, GNU make
URL	https://github.com/AbbVie-ComputationalGenomics/SAIGEgds

Suggests	parallel, markdown, rmarkdown, crayon, SNPRelate, RUnit, knitr, 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_2.7.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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