SKAT
SNP-Set (Sequence) Kernel Association Test

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SKAT: SNP-Set (Sequence) Kernel Association Test
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API

API for SKAT
SNP-Set (Sequence) Kernel Association Test

Global functions
Beta.Weights Source code
Beta_Weight Source code
Beta_Weights Source code
Check_Class Source code
Check_Duplicate Source code
Check_File_Exists Source code
Check_ID_Length Source code
Check_SetID_LOG Source code
Check_Sex_Var Source code
Close_SSD Man page Source code
Create_Temporaly_SetID Source code
Dist_Case Source code
Dist_Case_Control Source code
Dist_Control Source code
Generate_SSD_SetID Man page Source code
Generate_SSD_SetID_Work Source code
Generate_TestData Source code
Get_A Source code
Get_A_Q Source code
Get_B Source code
Get_B_Q Source code
Get_Beta Source code
Get_CausalSNPs Source code
Get_Critical_Value Source code
Get_Davies_PVal Man page Source code
Get_EffectiveNumberTest Man page Source code
Get_EffectiveNumberTest_Item Source code
Get_EffectiveNumberTest_Item_MidP Source code
Get_Genotypes_SSD Man page Source code
Get_Genotypes_SSD_Sparse Man page Source code
Get_Lambda Man page Source code
Get_Lambda_Approx Source code
Get_Lambda_U_From_Z Source code
Get_Liu_PVal Man page Source code
Get_Liu_PVal.MOD Source code
Get_Liu_PVal.MOD.Lambda Source code
Get_Liu_PVal.MOD.Lambda.Zero Source code
Get_Liu_Params Source code
Get_Liu_Params_Mod Source code
Get_Liu_Params_Mod_Lambda Source code
Get_Logistic_Weights Man page Source code
Get_Logistic_Weights_MAF Man page Source code
Get_MAF Source code
Get_Matrix_Square.1 Source code
Get_Optimal_rho_est Source code
Get_PI_New Source code
Get_PI_W_ALL Source code
Get_PValue Source code
Get_PValue.Lambda Source code
Get_Power_Continuous Source code
Get_Power_Continuous_R Source code
Get_Power_Corr.GetPower Source code
Get_Power_Corr_WR_rho Source code
Get_Power_Logistic Source code
Get_Power_Logistic_R Source code
Get_RandomRegion Source code
Get_RequiredSampleSize Man page
Get_RequiredSampleSize.SKAT_Power Source code
Get_RequiredSampleSize.numeric Source code
Get_RequiredSampleSize_OLD Source code
Get_Res_Arrays Source code
Get_Resample_P Source code
Get_Resampling_Bin Source code
Get_Resampling_Pvalue Man page Source code
Get_Resampling_Pvalue_1 Man page Source code
Get_SKAT_Residuals.Get_X1 Source code
Get_SKAT_Residuals.linear Source code
Get_SKAT_Residuals.logistic Source code
Get_Satterthwaite Source code
Get_Total_K Source code
Get_W_New Source code
Impute Source code
Impute_XChr Source code
Is_TryError Source code
K1_Help Source code
KMTest.linear.Linear Source code
KMTest.logistic.Linear Source code
KMTest.logistic.Linear.VarMatching Source code
Kill_SSD_SetID Source code
MSG_SKAT_Example Source code
Met_SKAT_Get_Pvalue Source code
Mk_SSD_ALL_Output Source code
Open_Plink Source code
Open_SSD Man page Source code
Power_Continuous Man page Source code
Power_Continuous_R Man page Source code
Power_Logistic Man page Source code
Power_Logistic_R Man page Source code
Print_Error_SSD Source code
Print_File_Info Source code
QQPlot_Adj Man page Source code
QQPlot_Adj_Simple Source code
Read_File_Info Source code
Read_File_Info_Head Source code
Read_Plink_FAM Man page Source code
Read_Plink_FAM_Cov Man page Source code
Read_SNP_WeightFile Man page Source code
Resampling_FWER Man page Source code
Resampling_FWER_1 Man page Source code
SKAT Man page Source code
SKAT.SSD.All Man page Source code
SKAT.SSD.GetSNP_Weight Source code
SKAT.SSD.OneSet Man page Source code
SKAT.SSD.OneSet_SetIndex Man page Source code
SKAT.SSD.OneSet_SetIndex_OLD Source code
SKAT.emma.eigen.R.wo.Z Source code
SKAT.example Man page
SKAT.example.ChrX Man page
SKAT.fam.example Man page
SKAT.haplotypes Man page
SKAT.linear Source code
SKAT.linear.Linear Source code
SKAT.linear.Other Source code
SKAT.logistic Source code
SKAT.logistic.Linear Source code
SKAT.logistic.Other Source code
SKATBinary Man page Source code
SKATBinary.SSD.All Man page Source code
SKATBinary.SSD.OneSet Man page Source code
SKATBinary.SSD.OneSet_SetIndex Man page Source code
SKATBinary.Single.CheckZ Source code
SKATBinary.example Man page
SKATBinary_RestoreSeed Source code
SKATBinary_Robust Man page Source code
SKATBinary_Robust.SSD.All Man page Source code
SKATBinary_Robust.SSD.OneSet Man page Source code
SKATBinary_Robust.SSD.OneSet_SetIndex Man page Source code
SKATBinary_SeedNum Source code
SKATBinary_Single Man page Source code
SKATExactBin Source code
SKATExactBin.Adaptive Source code
SKATExactBin.ComputProb_New Source code
SKATExactBin.ComputProb_Random Source code
SKATExactBin.ComputeProb_Group Source code
SKATExactBin.ER_R Source code
SKATExactBin.Firth Source code
SKATExactBin.GetQ Source code
SKATExactBin.Moment Source code
SKATExactBin.SKATO_GetQParam Source code
SKATExactBin.Work Source code
SKATExactBin.Work_Adaptive Source code
SKATExactBin_Check Source code
SKATExactBin_CheckAccuracy Source code
SKATExactBin_CheckObj Source code
SKATExactBin_SingleMAP Source code
SKATPermu Source code
SKAT_1 Source code
SKAT_2Kernel_Optimal_Get_Q Source code
SKAT_2Kernel_Ortho_Optimal_Each_Q Source code
SKAT_2Kernel_Ortho_Optimal_Get_Params_each_r Source code
SKAT_2Kernel_Ortho_Optimal_Get_Pvalue Source code
SKAT_2Kernel_Ortho_Optimal_Integrate_Func Source code
SKAT_2Kernel_Ortho_Optimal_PValue_Liu Source code
SKAT_2Kernel_Ortho_Optimal_Param Source code
SKAT_CR_Linear Source code
SKAT_CR_Optimal Source code
SKAT_Check_Method Man page Source code
SKAT_Check_RCorr Source code
SKAT_ChrX Man page Source code
SKAT_ChrY Man page Source code
SKAT_Code_XChr Source code
SKAT_CommonRare Man page Source code
SKAT_CommonRare.SSD.All Man page Source code
SKAT_CommonRare.SSD.OneSet Man page Source code
SKAT_CommonRare.SSD.OneSet_SetIndex Man page Source code
SKAT_CommonRare_Robust Man page Source code
SKAT_CommonRare_Robust.SSD.All Man page Source code
SKAT_CommonRare_Robust.SSD.OneSet Man page Source code
SKAT_CommonRare_Robust.SSD.OneSet_SetIndex Man page Source code
SKAT_GET_kurtosis Source code
SKAT_GET_skewness Source code
SKAT_Get_Cov_Param Source code
SKAT_Get_DF_Sim Source code
SKAT_Get_MAF Source code
SKAT_Get_Polymorphic_SNP Source code
SKAT_Get_Var_Elements Source code
SKAT_Logistic_PVal_QuantileAdj Source code
SKAT_Logistic_VarMatching_GetParam Source code
SKAT_Logistic_VarMatching_GetParam1 Source code
SKAT_Logistic_VarMatching_GetParam1_OnlySim Source code
SKAT_Logistic_VarMatching_GetParam1_QuantileAdj Source code
SKAT_Logistic_VarMatching_QuantileAdj_Param Source code
SKAT_MAIN_Check_OutType Source code
SKAT_MAIN_Check_Z Source code
SKAT_MAIN_Check_Z_Flip Source code
SKAT_MAIN_Check_Z_Impute Source code
SKAT_META_Optimal Source code
SKAT_META_Optimal_Get_Pvalue Source code
SKAT_META_Optimal_Get_Q Source code
SKAT_META_Optimal_Get_Q_Res Source code
SKAT_META_Optimal_Param Source code
SKAT_NULL_emmaX Man page Source code
SKAT_Null_Model Man page Source code
SKAT_Null_Model_ChrX Man page Source code
SKAT_Null_Model_Get_Includes Source code
SKAT_Null_Model_MomentAdjust Man page Source code
SKAT_Optimal_Each_Q Man page Source code
SKAT_Optimal_Each_Q_VarMatching Source code
SKAT_Optimal_GetZItem2 Source code
SKAT_Optimal_Get_Kertosis_Mixture Source code
SKAT_Optimal_Get_Pvalue Source code
SKAT_Optimal_Get_Pvalue_VarMatching Source code
SKAT_Optimal_Get_Q Source code
SKAT_Optimal_Integrate_Func_Davies Source code
SKAT_Optimal_Integrate_Func_Liu Source code
SKAT_Optimal_Integrate_Func_VarMatching Source code
SKAT_Optimal_Linear Source code
SKAT_Optimal_Logistic Source code
SKAT_Optimal_Logistic_VarMatching Source code
SKAT_Optimal_PValue_Davies Man page Source code
SKAT_Optimal_PValue_Liu Man page Source code
SKAT_Optimal_PValue_VarMatching Source code
SKAT_Optimal_Param Source code
SKAT_Optimal_Param_VarMatching Source code
SKAT_PValue_Logistic_VarMatching Source code
SKAT_RunFrom_MetaSKAT Source code
SKAT_Scale_Genotypes Source code
SKAT_With_NullModel Source code
SKAT_With_NullModel_ADJ Source code
SKAT_davies Source code
SKAT_emmaX Source code
SKAT_emmaX.SSD.All Source code
SKAT_emmaX.SSD.OneSet Source code
SKAT_emmaX.SSD.OneSet_SetIndex Source code
SKAT_emmaX_work Source code
SKAT_liu Source code
SKAT_liu.MOD Source code
SPA_ER_kernel Source code
SSD_FILE_OPEN.FileName Man page
SSD_FILE_OPEN.isOpen Man page
SingleSNP_INFO Source code
Sparse_Phi Source code
call_Kernel_2wayIX Source code
call_Kernel_IBS Source code
call_Kernel_IBS_Weight Source code
colMax Source code Source code
emma.delta.REML.LL.wo.Z Source code
emma.delta.REML.dLL.wo.Z Source code Source code
emma.eigen.R.wo.Z Source code
fast.invFisher Source code
lskmTest.GetKernel Source code
trace.SKAT Source code
SKAT documentation built on Jan. 15, 2023, 5:10 p.m.

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