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

## Documentation for package ‘SAIGEgds’ version 2.2.0

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

## 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-V tests
seqAssocGLMM_ACAT_V | ACAT-V tests
seqAssocGLMM_Burden | Burden tests
seqAssocGLMM_SKAT | SKAT tests
seqAssocGLMM_SPA | P-value calculation
seqFitDenseGRM | Sparse Genetic relationship matrix
seqFitLDpruning | LD pruning
seqFitNullGLMM_SPA | Fit the null model with GRM
seqFitSparseGRM | Sparse Genetic relationship matrix
seqSAIGE_LoadPval | Load the association results