SNP-Set (Sequence) Kernel Association Test


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Documentation for package ‘SKAT’ version 1.3.2.1

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Close_SSD Close SNP set data file (SSD)
Generate_SSD_SetID Generate SNP set data file (SSD)
Get_EffectiveNumberTest Estimate the effective number of tests for Bonferroni correction
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 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_Single Single variant tests for binary traits with Firth and efficient resampling methods
SKAT_ChrX SNP-set (Sequence) Kernel Association Test for X chromosome variables
SKAT_CommonRare SKAT for the combined effect of common and rare variants
SKAT_CommonRare.SSD.All SKAT for the combined effect of common and rare variants
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_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
SSD_FILE_OPEN.FileName Internal variables for SSD
SSD_FILE_OPEN.isOpen Internal variables for SSD