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] (<https://orcid.org/0000-0002-1390-0708>), Wei Zhou [ctb] (the original author of the SAIGE R package), J. Wade Davis [ctb]|
|Bioconductor views||Genetics Software StatisticalMethod|
|Maintainer||Xiuwen Zheng <[email protected]>|
|Package repository||View on Bioconductor|
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