SNP-set (Sequence) Kernel Association Test


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Documentation for package ‘SKAT’ version 0.82

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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 file
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_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