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sample size to achieve the given power", "topics": [ "Get_RequiredSampleSize" ] }, { "page": "Get_Resampling_Pvalue", "title": "Compute a resampling p-value", "topics": [ "Get_Resampling_Pvalue", "Get_Resampling_Pvalue_1" ] }, { "page": "Open_SSD", "title": "Open SNP set data file (SSD)", "topics": [ "Open_SSD" ] }, { "page": "Power_Continuous", "title": "Power calculation, continuous traits", "topics": [ "Power_Continuous", "Power_Continuous_R" ] }, { "page": "Power_Logistic", "title": "Power calculation, Dichotomous traits", "topics": [ "Power_Logistic", "Power_Logistic_R" ] }, { "page": "QQPlot_Adj", "title": "Adjusted QQ plot", "topics": [ "QQPlot_Adj" ] }, { "page": "Read_Plink_FAM", "title": "Read Plink FAM and covariates files", "topics": [ "Read_Plink_FAM", "Read_Plink_FAM_Cov" ] }, { "page": "Read_SNP_WeightFile", "title": "Read a file with custom weights", "topics": [ "Read_SNP_WeightFile" ] }, { "page": "Resampling_FWER", "title": "Obtain significant SNP sets after controlling family wise error rate (FWER)", "topics": [ "Resampling_FWER", "Resampling_FWER_1" ] }, { "page": "SKAT", "title": "SNP-set (Sequence) Kernel Association Test", "topics": [ "SKAT", "SKAT.SSD.OneSet", "SKAT.SSD.OneSet_SetIndex" ] }, { "page": "SKAT_ChrX", "title": "SNP-set (Sequence) Kernel Association Test for X and Y chromosome variables", "topics": [ "SKAT_ChrX", "SKAT_ChrY" ] }, { "page": "SKAT_CommonRare", "title": "SKAT for the combined effect of common and rare variants", "topics": [ "SKAT_CommonRare", "SKAT_CommonRare.SSD.OneSet", "SKAT_CommonRare.SSD.OneSet_SetIndex" ] }, { "page": "SKAT_CommonRare_Robust", "title": "SNP set test (both common and rare variants) for binary traits with robust region-based methods", "topics": [ "SKAT_CommonRare_Robust", "SKAT_CommonRare_Robust.SSD.OneSet", "SKAT_CommonRare_Robust.SSD.OneSet_SetIndex" ] }, { "page": "SKAT_NULL_emmaX", "title": "Get parameters and residuals from the null model with incorporating the kinship structure", "topics": [ "SKAT_NULL_emmaX" ] }, { "page": "SKAT_Null_Model", "title": "Get parameters and residuals from the NULL model", "topics": [ "SKAT_Null_Model", "SKAT_Null_Model_ChrX" ] }, { "page": "SKAT_Null_Model_MomentAdjust", "title": "Get parameters and residuals from the NULL model for small sample adjustment", "topics": [ "SKAT_Null_Model_MomentAdjust" ] }, { "page": "SKAT.example", "title": "Example data for SKAT", "topics": [ "SKAT.example" ] }, { "page": "SKAT.example.ChrX", "title": "Example data for SKAT", "topics": [ "SKAT.example.ChrX" ] }, { "page": "SKAT.fam.example", "title": "Example data for SKAT_NULL_emmaX", "topics": [ "SKAT.fam.example" ] }, { "page": "SKAT.haplotypes", "title": "Haplotype dataset for power calculation", "topics": [ "SKAT.haplotypes" ] }, { "page": "SKAT.SSD.All", "title": "SNP-set Kernel Association Test", "topics": [ "SKAT.SSD.All", "SKATBinary.SSD.All", "SKATBinary_Robust.SSD.All", "SKAT_CommonRare.SSD.All", "SKAT_CommonRare_Robust.SSD.All" ] }, { "page": "SKATBinary", "title": "SNP set test for binary traits with asymptotic and efficient resampling methods", "topics": [ "SKATBinary", "SKATBinary.SSD.OneSet", "SKATBinary.SSD.OneSet_SetIndex" ] }, { "page": "SKATBinary_Robust", "title": "SNP set test for binary traits with robust region-based methods", "topics": [ "SKATBinary_Robust", "SKATBinary_Robust.SSD.OneSet", "SKATBinary_Robust.SSD.OneSet_SetIndex" ] }, { "page": "SKATBinary_Single", "title": "Single variant tests for binary traits with Firth and efficient resampling methods", "topics": [ "SKATBinary_Single" ] }, { "page": "SKATBinary.example", "title": "Example data for SKAT", "topics": [ "SKATBinary.example" ] }, { "page": "SSD_FILE_OPEN", "title": "Internal variables for SSD and functions for other packages", "topics": [ "Get_Davies_PVal", "Get_Lambda", "Get_Liu_PVal", "SKAT_Check_Method", "SKAT_Optimal_Each_Q", "SKAT_Optimal_PValue_Davies", "SKAT_Optimal_PValue_Liu", "SSD_FILE_OPEN.FileName", "SSD_FILE_OPEN.isOpen" ] } 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