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

## Documentation for package ‘SAIGEgds’ version 2.12.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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-O tests
seqAssocGLMM_ACAT_O_GT | ACAT-O tests
seqAssocGLMM_ACAT_V | ACAT-V tests
seqAssocGLMM_Burden | Burden tests
seqAssocGLMM_GT | P-value calculation
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 for the SAIGE mixed model framework
seqFitSparseGRM | Sparse & dense genetic relationship matrix
seqGetGenoByGeno | Genotype-by-Genotype Interaction Matrix
seqRefitNullGLMM | Fit the null model for the SAIGE mixed model framework
seqSAIGE_LoadPval | Load the association results