R/RcppExports.R

In 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)

# Generated by using Rcpp::compileAttributes() -> do not edit by hand
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

SetSampleIdx_forGenetest_vcfDosage <- function(sample_idx, Ntest) {
    invisible(.Call('_SAIGE_SetSampleIdx_forGenetest_vcfDosage', PACKAGE = 'SAIGE', sample_idx, Ntest))
}

setMAFcutoffs <- function(minVal, maxVal) {
    invisible(.Call('_SAIGE_setMAFcutoffs', PACKAGE = 'SAIGE', minVal, maxVal))
}

setvcfDosageMatrix <- function(vcfFileName, vcfFileIndex, vcfField) {
    .Call('_SAIGE_setvcfDosageMatrix', PACKAGE = 'SAIGE', vcfFileName, vcfFileIndex, vcfField)
}

getNumofSamples_Matrix <- function() {
    .Call('_SAIGE_getNumofSamples_Matrix', PACKAGE = 'SAIGE')
}

getSampleIDlist_vcfMatrix <- function() {
    .Call('_SAIGE_getSampleIDlist_vcfMatrix', PACKAGE = 'SAIGE')
}

getGenoOfGene_vcf <- function(marker_group_line, minInfo) {
    .Call('_SAIGE_getGenoOfGene_vcf', PACKAGE = 'SAIGE', marker_group_line, minInfo)
}

closevcfDosageFile <- function() {
    invisible(.Call('_SAIGE_closevcfDosageFile', PACKAGE = 'SAIGE'))
}

closeGenoFile_plink <- function() {
    invisible(.Call('_SAIGE_closeGenoFile_plink', PACKAGE = 'SAIGE'))
}

gettotalMarker <- function() {
    .Call('_SAIGE_gettotalMarker', PACKAGE = 'SAIGE')
}

getAlleleFreqVec <- function() {
    .Call('_SAIGE_getAlleleFreqVec', PACKAGE = 'SAIGE')
}

getMACVec <- function() {
    .Call('_SAIGE_getMACVec', PACKAGE = 'SAIGE')
}

getSubMarkerIndex <- function() {
    .Call('_SAIGE_getSubMarkerIndex', PACKAGE = 'SAIGE')
}

getSubMarkerNum <- function() {
    .Call('_SAIGE_getSubMarkerNum', PACKAGE = 'SAIGE')
}

getNnomissingOut <- function() {
    .Call('_SAIGE_getNnomissingOut', PACKAGE = 'SAIGE')
}

getMsub_MAFge_minMAFtoConstructGRM <- function() {
    .Call('_SAIGE_getMsub_MAFge_minMAFtoConstructGRM', PACKAGE = 'SAIGE')
}

Get_MultiMarkersBySample_StdGeno_Mat <- function() {
    invisible(.Call('_SAIGE_Get_MultiMarkersBySample_StdGeno_Mat', PACKAGE = 'SAIGE'))
}

Get_MultiMarkersBySample_StdGeno <- function(markerIndexVec, stdGenoMultiMarkers) {
    invisible(.Call('_SAIGE_Get_MultiMarkersBySample_StdGeno', PACKAGE = 'SAIGE', markerIndexVec, stdGenoMultiMarkers))
}

parallelCrossProd <- function(bVec) {
    .Call('_SAIGE_parallelCrossProd', PACKAGE = 'SAIGE', bVec)
}

innerProductFun <- function(x, y) {
    .Call('_SAIGE_innerProductFun', PACKAGE = 'SAIGE', x, y)
}

parallelCrossProd_full <- function(bVec, markerNum) {
    .Call('_SAIGE_parallelCrossProd_full', PACKAGE = 'SAIGE', bVec, markerNum)
}

parallelCrossProd_LOCO <- function(bVec) {
    .Call('_SAIGE_parallelCrossProd_LOCO', PACKAGE = 'SAIGE', bVec)
}

setupSparseGRM <- function(r, locationMatinR, valueVecinR) {
    invisible(.Call('_SAIGE_setupSparseGRM', PACKAGE = 'SAIGE', r, locationMatinR, valueVecinR))
}

getCrossprodMatAndKin <- function(bVec) {
    .Call('_SAIGE_getCrossprodMatAndKin', PACKAGE = 'SAIGE', bVec)
}

getCrossprodMatAndKin_LOCO <- function(bVec) {
    .Call('_SAIGE_getCrossprodMatAndKin_LOCO', PACKAGE = 'SAIGE', bVec)
}

printComb <- function(N) {
    invisible(.Call('_SAIGE_printComb', PACKAGE = 'SAIGE', N))
}

findIndiceRelatedSample <- function() {
    invisible(.Call('_SAIGE_findIndiceRelatedSample', PACKAGE = 'SAIGE'))
}

parallelcalsparseGRM <- function(GRMvec) {
    invisible(.Call('_SAIGE_parallelcalsparseGRM', PACKAGE = 'SAIGE', GRMvec))
}

parallelsumTwoVec <- function(x) {
    invisible(.Call('_SAIGE_parallelsumTwoVec', PACKAGE = 'SAIGE', x))
}

setgeno <- function(genofile, subSampleInGeno, memoryChunk, isDiagofKinSetAsOne) {
    invisible(.Call('_SAIGE_setgeno', PACKAGE = 'SAIGE', genofile, subSampleInGeno, memoryChunk, isDiagofKinSetAsOne))
}

Get_OneSNP_Geno <- function(SNPIdx) {
    .Call('_SAIGE_Get_OneSNP_Geno', PACKAGE = 'SAIGE', SNPIdx)
}

Get_OneSNP_Geno_forVarianceRatio <- function(SNPIdx) {
    .Call('_SAIGE_Get_OneSNP_Geno_forVarianceRatio', PACKAGE = 'SAIGE', SNPIdx)
}

Get_OneSNP_StdGeno <- function(SNPIdx) {
    .Call('_SAIGE_Get_OneSNP_StdGeno', PACKAGE = 'SAIGE', SNPIdx)
}

getDiagOfSigma <- function(wVec, tauVec) {
    .Call('_SAIGE_getDiagOfSigma', PACKAGE = 'SAIGE', wVec, tauVec)
}

getDiagOfSigma_LOCO <- function(wVec, tauVec) {
    .Call('_SAIGE_getDiagOfSigma_LOCO', PACKAGE = 'SAIGE', wVec, tauVec)
}

getCrossprod <- function(bVec, wVec, tauVec) {
    .Call('_SAIGE_getCrossprod', PACKAGE = 'SAIGE', bVec, wVec, tauVec)
}

getCrossprod_LOCO <- function(bVec, wVec, tauVec) {
    .Call('_SAIGE_getCrossprod_LOCO', PACKAGE = 'SAIGE', bVec, wVec, tauVec)
}

gen_sp_GRM <- function() {
    .Call('_SAIGE_gen_sp_GRM', PACKAGE = 'SAIGE')
}

gen_sp_Sigma <- function(wVec, tauVec) {
    .Call('_SAIGE_gen_sp_Sigma', PACKAGE = 'SAIGE', wVec, tauVec)
}

gen_spsolve_v3 <- function(yvec) {
    .Call('_SAIGE_gen_spsolve_v3', PACKAGE = 'SAIGE', yvec)
}

gen_spsolve_v4 <- function(wVec, tauVec, yvec) {
    .Call('_SAIGE_gen_spsolve_v4', PACKAGE = 'SAIGE', wVec, tauVec, yvec)
}

setisUsePrecondM <- function(isUseSparseSigmaforPCG) {
    invisible(.Call('_SAIGE_setisUsePrecondM', PACKAGE = 'SAIGE', isUseSparseSigmaforPCG))
}

setisUseSparseSigmaforInitTau <- function(isUseSparseSigmaforInitTau0) {
    invisible(.Call('_SAIGE_setisUseSparseSigmaforInitTau', PACKAGE = 'SAIGE', isUseSparseSigmaforInitTau0))
}

setisUseSparseSigmaforNullModelFitting <- function(isUseSparseSigmaforModelFitting0) {
    invisible(.Call('_SAIGE_setisUseSparseSigmaforNullModelFitting', PACKAGE = 'SAIGE', isUseSparseSigmaforModelFitting0))
}

getPCG1ofSigmaAndVector <- function(wVec, tauVec, bVec, maxiterPCG, tolPCG) {
    .Call('_SAIGE_getPCG1ofSigmaAndVector', PACKAGE = 'SAIGE', wVec, tauVec, bVec, maxiterPCG, tolPCG)
}

getPCG1ofSigmaAndVector_old <- function(wVec, tauVec, bVec, maxiterPCG, tolPCG) {
    .Call('_SAIGE_getPCG1ofSigmaAndVector_old', PACKAGE = 'SAIGE', wVec, tauVec, bVec, maxiterPCG, tolPCG)
}

getPCG1ofSigmaAndVector_LOCO <- function(wVec, tauVec, bVec, maxiterPCG, tolPCG) {
    .Call('_SAIGE_getPCG1ofSigmaAndVector_LOCO', PACKAGE = 'SAIGE', wVec, tauVec, bVec, maxiterPCG, tolPCG)
}

set_seed <- function(seed) {
    invisible(.Call('_SAIGE_set_seed', PACKAGE = 'SAIGE', seed))
}

nb <- function(n) {
    .Call('_SAIGE_nb', PACKAGE = 'SAIGE', n)
}

setStartEndIndex <- function(startIndex, endIndex, chromIndex) {
    invisible(.Call('_SAIGE_setStartEndIndex', PACKAGE = 'SAIGE', startIndex, endIndex, chromIndex))
}

setStartEndIndexVec <- function(startIndex_vec, endIndex_vec) {
    invisible(.Call('_SAIGE_setStartEndIndexVec', PACKAGE = 'SAIGE', startIndex_vec, endIndex_vec))
}

calCV <- function(xVec) {
    .Call('_SAIGE_calCV', PACKAGE = 'SAIGE', xVec)
}

GetTrace <- function(Sigma_iX, Xmat, wVec, tauVec, cov1, nrun, maxiterPCG, tolPCG, traceCVcutoff) {
    .Call('_SAIGE_GetTrace', PACKAGE = 'SAIGE', Sigma_iX, Xmat, wVec, tauVec, cov1, nrun, maxiterPCG, tolPCG, traceCVcutoff)
}

getCoefficients <- function(Yvec, Xmat, wVec, tauVec, maxiterPCG, tolPCG) {
    .Call('_SAIGE_getCoefficients', PACKAGE = 'SAIGE', Yvec, Xmat, wVec, tauVec, maxiterPCG, tolPCG)
}

getCoefficients_LOCO <- function(Yvec, Xmat, wVec, tauVec, maxiterPCG, tolPCG) {
    .Call('_SAIGE_getCoefficients_LOCO', PACKAGE = 'SAIGE', Yvec, Xmat, wVec, tauVec, maxiterPCG, tolPCG)
}

getCoefficients_q_LOCO <- function(Yvec, Xmat, wVec, tauVec, maxiterPCG, tolPCG) {
    .Call('_SAIGE_getCoefficients_q_LOCO', PACKAGE = 'SAIGE', Yvec, Xmat, wVec, tauVec, maxiterPCG, tolPCG)
}

getAIScore <- function(Yvec, Xmat, wVec, tauVec, Sigma_iY, Sigma_iX, cov, nrun, maxiterPCG, tolPCG, traceCVcutoff) {
    .Call('_SAIGE_getAIScore', PACKAGE = 'SAIGE', Yvec, Xmat, wVec, tauVec, Sigma_iY, Sigma_iX, cov, nrun, maxiterPCG, tolPCG, traceCVcutoff)
}

fitglmmaiRPCG <- function(Yvec, Xmat, wVec, tauVec, Sigma_iY, Sigma_iX, cov, nrun, maxiterPCG, tolPCG, tol, traceCVcutoff) {
    .Call('_SAIGE_fitglmmaiRPCG', PACKAGE = 'SAIGE', Yvec, Xmat, wVec, tauVec, Sigma_iY, Sigma_iX, cov, nrun, maxiterPCG, tolPCG, tol, traceCVcutoff)
}

getSigma_X <- function(wVec, tauVec, Xmat, maxiterPCG, tolPCG) {
    .Call('_SAIGE_getSigma_X', PACKAGE = 'SAIGE', wVec, tauVec, Xmat, maxiterPCG, tolPCG)
}

getSigma_X_LOCO <- function(wVec, tauVec, Xmat, maxiterPCG, tolPCG) {
    .Call('_SAIGE_getSigma_X_LOCO', PACKAGE = 'SAIGE', wVec, tauVec, Xmat, maxiterPCG, tolPCG)
}

getSigma_G <- function(wVec, tauVec, Gvec, maxiterPCG, tolPCG) {
    .Call('_SAIGE_getSigma_G', PACKAGE = 'SAIGE', wVec, tauVec, Gvec, maxiterPCG, tolPCG)
}

getSigma_G_LOCO <- function(wVec, tauVec, Gvec, maxiterPCG, tolPCG) {
    .Call('_SAIGE_getSigma_G_LOCO', PACKAGE = 'SAIGE', wVec, tauVec, Gvec, maxiterPCG, tolPCG)
}

GetTrace_q <- function(Sigma_iX, Xmat, wVec, tauVec, cov1, nrun, maxiterPCG, tolPCG, traceCVcutoff) {
    .Call('_SAIGE_GetTrace_q', PACKAGE = 'SAIGE', Sigma_iX, Xmat, wVec, tauVec, cov1, nrun, maxiterPCG, tolPCG, traceCVcutoff)
}

getAIScore_q <- function(Yvec, Xmat, wVec, tauVec, Sigma_iY, Sigma_iX, cov, nrun, maxiterPCG, tolPCG, traceCVcutoff) {
    .Call('_SAIGE_getAIScore_q', PACKAGE = 'SAIGE', Yvec, Xmat, wVec, tauVec, Sigma_iY, Sigma_iX, cov, nrun, maxiterPCG, tolPCG, traceCVcutoff)
}

getAIScore_q_LOCO <- function(Yvec, Xmat, wVec, tauVec, nrun, maxiterPCG, tolPCG, traceCVcutoff) {
    .Call('_SAIGE_getAIScore_q_LOCO', PACKAGE = 'SAIGE', Yvec, Xmat, wVec, tauVec, nrun, maxiterPCG, tolPCG, traceCVcutoff)
}

fitglmmaiRPCG_q_LOCO <- function(Yvec, Xmat, wVec, tauVec, nrun, maxiterPCG, tolPCG, tol, traceCVcutoff) {
    .Call('_SAIGE_fitglmmaiRPCG_q_LOCO', PACKAGE = 'SAIGE', Yvec, Xmat, wVec, tauVec, nrun, maxiterPCG, tolPCG, tol, traceCVcutoff)
}

fitglmmaiRPCG_q <- function(Yvec, Xmat, wVec, tauVec, Sigma_iY, Sigma_iX, cov, nrun, maxiterPCG, tolPCG, tol, traceCVcutoff) {
    .Call('_SAIGE_fitglmmaiRPCG_q', PACKAGE = 'SAIGE', Yvec, Xmat, wVec, tauVec, Sigma_iY, Sigma_iX, cov, nrun, maxiterPCG, tolPCG, tol, traceCVcutoff)
}

parallelCrossProd_usingSubMarker <- function(bVec) {
    .Call('_SAIGE_parallelCrossProd_usingSubMarker', PACKAGE = 'SAIGE', bVec)
}

getCrossprodMatAndKin_usingSubMarker <- function(bVec) {
    .Call('_SAIGE_getCrossprodMatAndKin_usingSubMarker', PACKAGE = 'SAIGE', bVec)
}

parallelInnerProduct <- function(x, y) {
    .Call('_SAIGE_parallelInnerProduct', PACKAGE = 'SAIGE', x, y)
}

calGRMValueforSamplePair <- function(sampleidsVec) {
    .Call('_SAIGE_calGRMValueforSamplePair', PACKAGE = 'SAIGE', sampleidsVec)
}

createSparseKin <- function(markerIndexVec, relatednessCutoff, wVec, tauVec) {
    .Call('_SAIGE_createSparseKin', PACKAGE = 'SAIGE', markerIndexVec, relatednessCutoff, wVec, tauVec)
}

getColfromStdGenoMultiMarkersMat <- function(a) {
    .Call('_SAIGE_getColfromStdGenoMultiMarkersMat', PACKAGE = 'SAIGE', a)
}

getNColStdGenoMultiMarkersMat <- function() {
    .Call('_SAIGE_getNColStdGenoMultiMarkersMat', PACKAGE = 'SAIGE')
}

getNRowStdGenoMultiMarkersMat <- function() {
    .Call('_SAIGE_getNRowStdGenoMultiMarkersMat', PACKAGE = 'SAIGE')
}

setSubMarkerIndex <- function(subMarkerIndexRandom) {
    invisible(.Call('_SAIGE_setSubMarkerIndex', PACKAGE = 'SAIGE', subMarkerIndexRandom))
}

setRelatednessCutoff <- function(a) {
    invisible(.Call('_SAIGE_setRelatednessCutoff', PACKAGE = 'SAIGE', a))
}

innerProduct <- function(x, y) {
    .Call('_SAIGE_innerProduct', PACKAGE = 'SAIGE', x, y)
}

refineKin <- function(relatednessCutoff) {
    .Call('_SAIGE_refineKin', PACKAGE = 'SAIGE', relatednessCutoff)
}

shortenList <- function(iMat, kinValueVecTemp, relatednessCutoff, wVec, tauVec) {
    .Call('_SAIGE_shortenList', PACKAGE = 'SAIGE', iMat, kinValueVecTemp, relatednessCutoff, wVec, tauVec)
}

testTime <- function(i, m_bVec) {
    .Call('_SAIGE_testTime', PACKAGE = 'SAIGE', i, m_bVec)
}

gen_sp_v2 <- function(a) {
    .Call('_SAIGE_gen_sp_v2', PACKAGE = 'SAIGE', a)
}

gen_spsolve_v2 <- function(a) {
    .Call('_SAIGE_gen_spsolve_v2', PACKAGE = 'SAIGE', a)
}

gen_spsolve_inR <- function(a, y) {
    .Call('_SAIGE_gen_spsolve_inR', PACKAGE = 'SAIGE', a, y)
}

get_DiagofKin <- function() {
    .Call('_SAIGE_get_DiagofKin', PACKAGE = 'SAIGE')
}

getstdgenoVectorScalorProduct <- function(jth, y, prodVec) {
    invisible(.Call('_SAIGE_getstdgenoVectorScalorProduct', PACKAGE = 'SAIGE', jth, y, prodVec))
}

sumPz <- function(Pbvec, Ubvec, mmchunksize) {
    invisible(.Call('_SAIGE_sumPz', PACKAGE = 'SAIGE', Pbvec, Ubvec, mmchunksize))
}

mmGetPb_MbyN <- function(cthchunk, mmchunksize, bvec, Pbvec, kinbvec) {
    invisible(.Call('_SAIGE_mmGetPb_MbyN', PACKAGE = 'SAIGE', cthchunk, mmchunksize, bvec, Pbvec, kinbvec))
}

mmGetPb_NbyM <- function(cthchunk, mmchunksize, bvec, Pbvec) {
    invisible(.Call('_SAIGE_mmGetPb_NbyM', PACKAGE = 'SAIGE', cthchunk, mmchunksize, bvec, Pbvec))
}

muliplyMailman <- function(bvec, Gbvec, kinbvec) {
    invisible(.Call('_SAIGE_muliplyMailman', PACKAGE = 'SAIGE', bvec, Gbvec, kinbvec))
}

muliplyMailman_NbyM <- function(bvec, tGbvec) {
    invisible(.Call('_SAIGE_muliplyMailman_NbyM', PACKAGE = 'SAIGE', bvec, tGbvec))
}

freqOverStd <- function(freqOverStdVec) {
    invisible(.Call('_SAIGE_freqOverStd', PACKAGE = 'SAIGE', freqOverStdVec))
}

getCrossprodMatAndKin_mailman <- function(bVec) {
    .Call('_SAIGE_getCrossprodMatAndKin_mailman', PACKAGE = 'SAIGE', bVec)
}

get_GRMdiagVec <- function() {
    .Call('_SAIGE_get_GRMdiagVec', PACKAGE = 'SAIGE')
}

setminMAFforGRM <- function(minMAFforGRM) {
    invisible(.Call('_SAIGE_setminMAFforGRM', PACKAGE = 'SAIGE', minMAFforGRM))
}

set_Diagof_StdGeno_LOCO <- function() {
    invisible(.Call('_SAIGE_set_Diagof_StdGeno_LOCO', PACKAGE = 'SAIGE'))
}

setIsDropMissingDosages_bgen <- function(isdropmissingdosages) {
    invisible(.Call('_SAIGE_setIsDropMissingDosages_bgen', PACKAGE = 'SAIGE', isdropmissingdosages))
}

setgenoTest_bgenDosage <- function(filename, index_filename, ranges_to_include, ranges_to_exclude, ids_to_include, ids_to_exclude) {
    .Call('_SAIGE_setgenoTest_bgenDosage', PACKAGE = 'SAIGE', filename, index_filename, ranges_to_include, ranges_to_exclude, ids_to_include, ids_to_exclude)
}

getDosage_inner_bgen_withquery <- function() {
    .Call('_SAIGE_getDosage_inner_bgen_withquery', PACKAGE = 'SAIGE')
}

getDosage_inner_bgen_withquery_new <- function() {
    .Call('_SAIGE_getDosage_inner_bgen_withquery_new', PACKAGE = 'SAIGE')
}

getDosage_inner_bgen_withquery_new_Sparse <- function() {
    .Call('_SAIGE_getDosage_inner_bgen_withquery_new_Sparse', PACKAGE = 'SAIGE')
}

getDosage_bgen_withquery <- function() {
    .Call('_SAIGE_getDosage_bgen_withquery', PACKAGE = 'SAIGE')
}

getDosage_bgen_withquery_Sparse <- function() {
    .Call('_SAIGE_getDosage_bgen_withquery_Sparse', PACKAGE = 'SAIGE')
}

getDosage_bgen_noquery <- function() {
    .Call('_SAIGE_getDosage_bgen_noquery', PACKAGE = 'SAIGE')
}

getQueryStatus <- function() {
    .Call('_SAIGE_getQueryStatus', PACKAGE = 'SAIGE')
}

getisReadVariantBgen <- function() {
    .Call('_SAIGE_getisReadVariantBgen', PACKAGE = 'SAIGE')
}

getMarkerInfo <- function() {
    .Call('_SAIGE_getMarkerInfo', PACKAGE = 'SAIGE')
}

SetSampleIdx <- function(sample_idx, Ntest) {
    invisible(.Call('_SAIGE_SetSampleIdx', PACKAGE = 'SAIGE', sample_idx, Ntest))
}

closetestGenoFile_bgenDosage <- function() {
    invisible(.Call('_SAIGE_closetestGenoFile_bgenDosage', PACKAGE = 'SAIGE'))
}

setgenoTest_bgenDosage_v2 <- function(filename, index_filename, ranges_to_include, ranges_to_exclude, ids_to_include, ids_to_exclude) {
    .Call('_SAIGE_setgenoTest_bgenDosage_v2', PACKAGE = 'SAIGE', filename, index_filename, ranges_to_include, ranges_to_exclude, ids_to_include, ids_to_exclude)
}

getSampleSizeinBgen <- function() {
    .Call('_SAIGE_getSampleSizeinBgen', PACKAGE = 'SAIGE')
}

SetSampleIdx_vcfDosage <- function(sample_idx, Ntest) {
    invisible(.Call('_SAIGE_SetSampleIdx_vcfDosage', PACKAGE = 'SAIGE', sample_idx, Ntest))
}

setTestField <- function(testFieldInput) {
    invisible(.Call('_SAIGE_setTestField', PACKAGE = 'SAIGE', testFieldInput))
}

setIsDropMissingDosages_vcf <- function(isdropmissingdosages) {
    invisible(.Call('_SAIGE_setIsDropMissingDosages_vcf', PACKAGE = 'SAIGE', isdropmissingdosages))
}

setgenoTest_vcfDosage <- function(vcfFileName, vcfFileIndex, vcfField, ids_to_exclude_vcf, ids_to_include_vcf, chromNam, start = 0L, end = 0L) {
    .Call('_SAIGE_setgenoTest_vcfDosage', PACKAGE = 'SAIGE', vcfFileName, vcfFileIndex, vcfField, ids_to_exclude_vcf, ids_to_include_vcf, chromNam, start, end)
}

getNumofSamples <- function() {
    .Call('_SAIGE_getNumofSamples', PACKAGE = 'SAIGE')
}

getSampleIDlist <- function() {
    .Call('_SAIGE_getSampleIDlist', PACKAGE = 'SAIGE')
}

getGenoOfnthVar_vcfDosage_pre <- function() {
    .Call('_SAIGE_getGenoOfnthVar_vcfDosage_pre', PACKAGE = 'SAIGE')
}

getGenoOfnthVar_vcfDosage <- function(mth) {
    .Call('_SAIGE_getGenoOfnthVar_vcfDosage', PACKAGE = 'SAIGE', mth)
}

closetestGenoFile_vcfDosage <- function() {
    invisible(.Call('_SAIGE_closetestGenoFile_vcfDosage', PACKAGE = 'SAIGE'))
}

getSampleSizeinVCF <- function() {
    .Call('_SAIGE_getSampleSizeinVCF', PACKAGE = 'SAIGE')
}

eigenMapMatMult <- function(A, B) {
    .Call('_SAIGE_eigenMapMatMult', PACKAGE = 'SAIGE', A, B)
}

mult_sp_sp_to_sp <- function(a, b) {
    .Call('_SAIGE_mult_sp_sp_to_sp', PACKAGE = 'SAIGE', a, b)
}

mult_sp_den_to_sp <- function(a, b) {
    .Call('_SAIGE_mult_sp_den_to_sp', PACKAGE = 'SAIGE', a, b)
}

mult_den_sp_to_sp <- function(a, b) {
    .Call('_SAIGE_mult_den_sp_to_sp', PACKAGE = 'SAIGE', a, b)
}

gen_sp <- function(a) {
    .Call('_SAIGE_gen_sp', PACKAGE = 'SAIGE', a)
}