# SNP-set (Sequence) Kernel Association Test

## Documentation for package ‘SKAT’ version 0.95

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

Close_SSD | Close SNP set data file (SSD)
Generate_SSD_SetID | Generate SNP set data file (SSD)
Get_Genotypes_SSD | Get Genotype data from SSD file
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 the resampling p-value
Get_Resampling_Pvalue_1 | Compute the 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
Read_Plink_FAM | Read a Plink FAM and covariates files
Read_Plink_FAM_Cov | Read a Plink FAM and covariates files
Read_SNP_WeightFile | Read a file with custom weights
Resampling_FWER | Return significant SNP sets after controlling family wise error rate (FWER)
Resampling_FWER_1 | Return significant SNP sets after controlling family wise error rate (FWER)
SKAT | SNP-set (Sequence) Kernel Association Test
SKAT.example | Example data for SKAT
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
SKAT_CommonRare | SKAT for the combined effect of rare and common variants
SKAT_CommonRare.SSD.All | SKAT for the combined effect of rare and common variants
SKAT_CommonRare.SSD.OneSet | SKAT for the combined effect of rare and common variants
SKAT_CommonRare.SSD.OneSet_SetIndex | SKAT for the combined effect of rare and common variants
SKAT_Null_Model | Get parameters and residuals from the H0 model
SKAT_Null_Model_MomentAdjust | Get parameters and residuals from the H0 model for small sample adjustment
SSD_FILE_OPEN.FileName | Interval variables for SSD files
SSD_FILE_OPEN.isOpen | Interval variables for SSD files