# SNP-Set (Sequence) Kernel Association Test

## Documentation for package ‘SKAT’ version 2.2.5

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

## Help Pages

Close_SSD | Close SNP set data file (SSD)
Generate_SSD_SetID | Generate SNP set data file (SSD)
Get_Davies_PVal | Internal variables for SSD and functions for other packages
Get_EffectiveNumberTest | Estimate the effective number of tests for Bonferroni correction
Get_Genotypes_SSD | Get Genotype data from SSD file
Get_Genotypes_SSD_Sparse | Get Genotype data from SSD file
Get_Lambda | Internal variables for SSD and functions for other packages
Get_Liu_PVal | Internal variables for SSD and functions for other packages
Get_Logistic_Weights | Get the logistic weight
Get_Logistic_Weights_MAF | Get the logistic weight
Get_RequiredSampleSize | Get the required sample size to achieve the given power
Get_Resampling_Pvalue | Compute a resampling p-value
Get_Resampling_Pvalue_1 | Compute a resampling p-value
Open_SSD | Open SNP set data file (SSD)
Power_Continuous | Power calculation, continuous traits
Power_Continuous_R | Power calculation, continuous traits
Power_Logistic | Power calculation, Dichotomous traits
Power_Logistic_R | Power calculation, Dichotomous traits
QQPlot_Adj | Adjusted QQ plot
Read_Plink_FAM | Read Plink FAM and covariates files
Read_Plink_FAM_Cov | Read Plink FAM and covariates files
Read_SNP_WeightFile | Read a file with custom weights
Resampling_FWER | Obtain significant SNP sets after controlling family wise error rate (FWER)
Resampling_FWER_1 | Obtain significant SNP sets after controlling family wise error rate (FWER)
SKAT | SNP-set (Sequence) Kernel Association Test
SKAT.example | Example data for SKAT
SKAT.example.ChrX | Example data for SKAT
SKAT.fam.example | Example data for SKAT_NULL_emmaX
SKAT.haplotypes | Haplotype dataset for power calculation
SKAT.SSD.All | SNP-set Kernel Association Test
SKAT.SSD.OneSet | SNP-set (Sequence) Kernel Association Test
SKAT.SSD.OneSet_SetIndex | SNP-set (Sequence) Kernel Association Test
SKATBinary | SNP set test for binary traits with asymptotic and efficient resampling methods
SKATBinary.example | Example data for SKAT
SKATBinary.SSD.All | SNP-set Kernel Association Test
SKATBinary.SSD.OneSet | SNP set test for binary traits with asymptotic and efficient resampling methods
SKATBinary.SSD.OneSet_SetIndex | SNP set test for binary traits with asymptotic and efficient resampling methods
SKATBinary_Robust | SNP set test for binary traits with robust region-based methods
SKATBinary_Robust.SSD.All | SNP-set Kernel Association Test
SKATBinary_Robust.SSD.OneSet | SNP set test for binary traits with robust region-based methods
SKATBinary_Robust.SSD.OneSet_SetIndex | SNP set test for binary traits with robust region-based methods
SKATBinary_Single | Single variant tests for binary traits with Firth and efficient resampling methods
SKAT_Check_Method | Internal variables for SSD and functions for other packages
SKAT_ChrX | SNP-set (Sequence) Kernel Association Test for X and Y chromosome variables
SKAT_ChrY | SNP-set (Sequence) Kernel Association Test for X and Y chromosome variables
SKAT_CommonRare | SKAT for the combined effect of common and rare variants
SKAT_CommonRare.SSD.All | SNP-set Kernel Association Test
SKAT_CommonRare.SSD.OneSet | SKAT for the combined effect of common and rare variants
SKAT_CommonRare.SSD.OneSet_SetIndex | SKAT for the combined effect of common and rare variants
SKAT_CommonRare_Robust | SNP set test (both common and rare variants) for binary traits with robust region-based methods
SKAT_CommonRare_Robust.SSD.All | SNP-set Kernel Association Test
SKAT_CommonRare_Robust.SSD.OneSet | SNP set test (both common and rare variants) for binary traits with robust region-based methods
SKAT_CommonRare_Robust.SSD.OneSet_SetIndex | SNP set test (both common and rare variants) for binary traits with robust region-based methods
SKAT_NULL_emmaX | Get parameters and residuals from the null model with incorporating the kinship structure
SKAT_Null_Model | Get parameters and residuals from the NULL model
SKAT_Null_Model_ChrX | Get parameters and residuals from the NULL model
SKAT_Null_Model_MomentAdjust | Get parameters and residuals from the NULL model for small sample adjustment
SKAT_Optimal_Each_Q | Internal variables for SSD and functions for other packages
SKAT_Optimal_PValue_Davies | Internal variables for SSD and functions for other packages
SKAT_Optimal_PValue_Liu | Internal variables for SSD and functions for other packages
SSD_FILE_OPEN.FileName | Internal variables for SSD and functions for other packages
SSD_FILE_OPEN.isOpen | Internal variables for SSD and functions for other packages