SNP-Set (Sequence) Kernel Association Test
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Documentation for package ‘SKAT’ version 2.2.5
Help Pages
| 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 |