SAIGEgds

This package is for version 3.10 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: 3.10

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 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 original SAIGE R package (v0.29.4.4). SAIGEgds also implements some of the SPAtest functions in C to speed up the calculation of Saddlepoint approximation. Benchmarks show that SAIGEgds is 5 to 6 times faster than the original 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 "3.6") 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 HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Genetics, Software, StatisticalMethod
Version 1.0.2
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License GPL-3
Depends R (>= 3.5.0), gdsfmt(>= 1.20.0), SeqArray(>= 1.24.1), Rcpp
Imports methods, stats, utils, RcppParallel, SPAtest (>= 3.0.0)
System Requirements C++11, GNU make
URL https://github.com/AbbVie-ComputationalGenomics/SAIGEgds
See More
Suggests parallel, crayon, RUnit, knitr, BiocGenerics, SNPRelate
Linking To Rcpp, RcppArmadillo, RcppParallel
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_1.0.2.tar.gz
Windows Binary SAIGEgds_1.0.2.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) SAIGEgds_1.0.2.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 3.10 Source Archive