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 |