SAIGEgds
This package is for version 3.11 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: 3.11
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("SAIGEgds")):
Installation
To install this package, start R (version "4.0") 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 | ||
| NEWS | Text |
Details
| biocViews | Genetics, Software, StatisticalMethod |
| Version | 1.2.3 |
| 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_1.2.3.tar.gz |
| Windows Binary | SAIGEgds_1.2.3.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | SAIGEgds_1.2.3.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 3.11 | Source Archive |