Package: SAIGEgds
Type: Package
Title: Scalable Implementation of Generalized mixed models using GDS
        files in PheWAS
Version: 1.0.0
Date: 2019-10-13
Depends: R (>= 3.5.0), gdsfmt (>= 1.20.0), SeqArray (>= 1.24.1), Rcpp
LinkingTo: Rcpp, RcppArmadillo, RcppParallel
Imports: methods, stats, utils, RcppParallel, SPAtest (>= 3.0.0)
Suggests: parallel, crayon, RUnit, knitr, BiocGenerics, SNPRelate
Authors@R: c(person("Xiuwen", "Zheng", role=c("aut", "cre"),
        email="xiuwen.zheng@abbvie.com", comment=c(ORCID="0000-0002-1390-0708")),
        person("Wei", "Zhou", role="ctb",
        comment="the original author of the SAIGE R package"),
        person("J. Wade", "Davis", role="ctb"))
Description: 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.
License: GPL-3
SystemRequirements: C++11, GNU make
VignetteBuilder: knitr
ByteCompile: TRUE
URL: https://github.com/AbbVie-ComputationalGenomics/SAIGEgds
biocViews: Software, Genetics, StatisticalMethod
git_url: https://git.bioconductor.org/packages/SAIGEgds
git_branch: RELEASE_3_10
git_last_commit: ba30b24
git_last_commit_date: 2019-10-29
Date/Publication: 2019-10-29
NeedsCompilation: yes
Packaged: 2019-10-30 03:53:48 UTC; biocbuild
Author: Xiuwen Zheng [aut, cre] (<https://orcid.org/0000-0002-1390-0708>),
  Wei Zhou [ctb] (the original author of the SAIGE R package),
  J. Wade Davis [ctb]
Maintainer: Xiuwen Zheng <xiuwen.zheng@abbvie.com>
Built: R 3.6.1; x86_64-apple-darwin13.4.0; 2019-11-01 09:38:44 UTC; unix
