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

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Documentation for package ‘SAIGEgds’ version 2.9.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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SAIGEgds-package	Scalable Implementation of Generalized mixed models in Phenome-Wide Association Studies using GDS files
glmmHeritability	Heritability estimation
pACAT	Cauchy Combination Test
pACAT2	Cauchy Combination Test
SAIGEgds	Scalable Implementation of Generalized mixed models in Phenome-Wide Association Studies using GDS files
seqAssocGLMM_ACAT_O	ACAT-V tests
seqAssocGLMM_ACAT_V	ACAT-V tests
seqAssocGLMM_Burden	Burden tests
seqAssocGLMM_SKAT	SKAT tests
seqAssocGLMM_SPA	P-value calculation
seqFitDenseGRM	Sparse & dense genetic relationship matrix
seqFitLDpruning	Linkage disequilibrium pruning
seqFitNullGLMM_SPA	Fit the null model with GRM
seqFitSparseGRM	Sparse & dense genetic relationship matrix
seqSAIGE_LoadPval	Load the association results