SKAT

Close SNP set data file (SSD)

Generate SNP set data file (SSD)

Estimate the effective number of tests for Bonferroni correction

Get Genotype data from SSD file

Get the logistic weight

Get the required sample size to achieve the given power

Compute a resampling p-value

Open SNP set data file (SSD)

Power calculation, continuous traits

Power calculation, Dichotomous traits

Adjusted QQ plot

Read Plink FAM and covariates files

Read a file with custom weights

Obtain significant SNP sets after controlling family wise error rate (FWER)

SNP-set (Sequence) Kernel Association Test

SNP-set Kernel Association Test

Example data for SKAT

Example data for SKAT

Example data for SKAT_NULL_emmaX

Haplotype dataset for power calculation

SNP set test for binary traits with asymptotic and efficient resampling methods

Example data for SKAT

SNP set test for binary traits with robust region-based methods

Single variant tests for binary traits with Firth and efficient resampling methods

SNP-set (Sequence) Kernel Association Test for X chromosome variables

SKAT for the combined effect of common and rare variants

SNP set test (both common and rare variants) for binary traits with robust region-based methods

Get parameters and residuals from the null model with incorporating the kinship structure

Get parameters and residuals from the NULL model

Get parameters and residuals from the NULL model for small sample adjustment

Internal variables for SSD and functions for other packages