weizhouUMICH/SAIGE
Efficiently controlling for case-control imbalance and sample relatedness in single-variant assoc tests (SAIGE) and controlling for sample relatedness in region-based assoc tests in large cohorts and biobanks (SAIGE-GENE)

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183
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41
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weizhouUMICH/SAIGE: Efficiently controlling for case-control imbalance and sample relatedness in single-variant assoc tests (SAIGE) and controlling for sample relatedness in region-based assoc tests in large cohorts and biobanks (SAIGE-GENE)
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API for weizhouUMICH/SAIGE
Efficiently controlling for case-control imbalance and sample relatedness in single-variant assoc tests (SAIGE) and controlling for sample relatedness in region-based assoc tests in large cohorts and biobanks (SAIGE-GENE)

Global functions
Beta_Weight Source code
CCT Man page Source code
Covariate_Transform Source code
Covariate_Transform_Back Source code
GetTrace Source code
GetTrace_q Source code
Get_Coef Source code
Get_Coef_LOCO Source code
Get_MultiMarkersBySample_StdGeno Source code
Get_MultiMarkersBySample_StdGeno_Mat Source code
Get_OneSNP_Geno Source code
Get_OneSNP_Geno_forVarianceRatio Source code
Get_OneSNP_StdGeno Source code
Related_ER Source code
SAIGE_SKAT_withRatioVec Source code
SKATtest_usingSKATLib Man page Source code
SPAGMMATtest Man page Source code
SPA_ER_kernel_related Source code
SPA_ER_kernel_related_Phiadj Source code
Saddle_Prob_q Source code
ScoreTest_NULL_Model Source code
Score_Test Source code
Score_Test_Sparse Source code
SetSampleIdx Source code
SetSampleIdx_forGenetest_vcfDosage Source code
SetSampleIdx_vcfDosage Source code
bigGRMPar Source code
bigGRMPar_new Source code
calCV Source code
calGRMValueforSamplePair Source code
checkPerfectSep Source code
closeGenoFile_plink Source code
closetestGenoFile_bgenDosage Source code
closetestGenoFile_vcfDosage Source code
closevcfDosageFile Source code
createSparseGRM Man page Source code
createSparseKin Source code
createSparseKinParallel Source code
eigenMapMatMult Source code
findIndiceRelatedSample Source code
fitNULLGLMM Man page Source code
fit_SKAT_NULL Man page Source code
fitglmmaiRPCG Source code
fitglmmaiRPCG_q Source code
fitglmmaiRPCG_q_LOCO Source code
freqOverStd Source code
gen_sp Source code
gen_sp_GRM Source code
gen_sp_Sigma Source code
gen_sp_v2 Source code
gen_spsolve_inR Source code
gen_spsolve_v2 Source code
gen_spsolve_v3 Source code
gen_spsolve_v4 Source code
getAIScore Source code
getAIScore_q Source code
getAIScore_q_LOCO Source code
getAlleleFreqVec Source code
getCateVarRatio_indVec Source code
getCoefficients Source code
getCoefficients_LOCO Source code
getCoefficients_q_LOCO Source code
getColfromStdGenoMultiMarkersMat Source code
getCovM_nopcg Source code
getCovMandOUT_cond Source code
getCovMandOUT_cond_pre Source code
getCrossprod Source code
getCrossprodMatAndKin Source code
getCrossprodMatAndKin_LOCO Source code
getCrossprodMatAndKin_mailman Source code
getCrossprodMatAndKin_usingSubMarker Source code
getCrossprod_LOCO Source code
getDiagOfSigma Source code
getDiagOfSigma_LOCO Source code
getDosage_bgen_noquery Source code
getDosage_bgen_withquery Source code
getDosage_bgen_withquery_Sparse Source code
getDosage_inner_bgen_withquery Source code
getDosage_inner_bgen_withquery_new Source code
getDosage_inner_bgen_withquery_new_Sparse Source code
getGenoOfGene_bgen Source code
getGenoOfGene_bgen_Sparse Source code
getGenoOfGene_vcf Source code
getGenoOfnthVar_vcfDosage Source code
getGenoOfnthVar_vcfDosage_pre Source code
getMACVec Source code
getMarkerInfo Source code
getMsub_MAFge_minMAFtoConstructGRM Source code
getNColStdGenoMultiMarkersMat Source code
getNRowStdGenoMultiMarkersMat Source code
getNeff Source code
getNnomissingOut Source code
getNumofSamples Source code
getNumofSamples_Matrix Source code
getPCG1ofSigmaAndVector Source code
getPCG1ofSigmaAndVector_LOCO Source code
getPCG1ofSigmaAndVector_old Source code
getQueryStatus Source code
getSampleIDlist Source code
getSampleIDlist_vcfMatrix Source code
getSampleSizeinBgen Source code
getSampleSizeinVCF Source code
getSigma_G Source code
getSigma_G_LOCO Source code
getSigma_X Source code
getSigma_X_LOCO Source code
getSparseSigma Source code
getSubMarkerIndex Source code
getSubMarkerNum Source code
get_DiagofKin Source code
get_GRMdiagVec Source code
get_absence_or_presence Source code
getcovM Source code
getisReadVariantBgen Source code
getstdgenoVectorScalorProduct Source code
gettotalMarker Source code
glmmkin.ai_PCG_Rcpp_Binary Source code
glmmkin.ai_PCG_Rcpp_Quantitative Source code
innerProduct Source code
innerProductFun Source code
mmGetPb_MbyN Source code
mmGetPb_NbyM Source code
muliplyMailman Source code
muliplyMailman_NbyM Source code
mult_den_sp_to_sp Source code
mult_sp_den_to_sp Source code
mult_sp_sp_to_sp Source code
nb Source code
outputDiagGRM Source code
parallelCrossProd Source code
parallelCrossProd_LOCO Source code
parallelCrossProd_full Source code
parallelCrossProd_usingSubMarker Source code
parallelInnerProduct Source code
parallelcalsparseGRM Source code
parallelsumTwoVec Source code
printComb Source code
processMale_XnonPAR Source code
refineKin Source code
refineKinPar Source code
scoreTest_SAIGE_binaryTrait Source code
scoreTest_SAIGE_binaryTrait_cond Source code
scoreTest_SAIGE_binaryTrait_cond_sparseSigma Source code
scoreTest_SAIGE_quantitativeTrait Source code
scoreTest_SAIGE_quantitativeTrait_old Source code
scoreTest_SAIGE_quantitativeTrait_sparseSigma Source code
scoreTest_SPAGMMAT_binaryTrait Source code
scoreTest_SPAGMMAT_binaryTrait_cond Source code
scoreTest_SPAGMMAT_binaryTrait_cond_sparseSigma Source code
scoreTest_SPAGMMAT_forVarianceRatio_binaryTrait Source code
scoreTest_SPAGMMAT_forVarianceRatio_quantitativeTrait Source code
setIsDropMissingDosages_bgen Source code
setIsDropMissingDosages_vcf Source code
setMAFcutoffs Source code
setRelatednessCutoff Source code
setStartEndIndex Source code
setStartEndIndexVec Source code
setSubMarkerIndex Source code
setTestField Source code
set_Diagof_StdGeno_LOCO Source code
set_seed Source code
setgeno Source code
setgenoTest_bgenDosage Source code
setgenoTest_bgenDosage_v2 Source code
setgenoTest_vcfDosage Source code
setisUsePrecondM Source code
setisUseSparseSigmaforInitTau Source code
setisUseSparseSigmaforNullModelFitting Source code
setminMAFforGRM Source code
setupSparseGRM Source code
setvcfDosageMatrix Source code
shortenList Source code
solveSpMatrixUsingArma Source code
subsetModelFileforMissing Source code
sumPz Source code
testTime Source code
test_stdGeno Source code
weizhouUMICH/SAIGE documentation built on May 6, 2022, 12:34 a.m.

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