pecotmr/R/cpp11.R at main · StatFunGen/pecotmr · GitHub

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# Generated by cpp11: do not edit by hand

bgenDosageCpp <- function(data, nSamples, alleles) {
  .Call(`_pecotmr_bgenDosageCpp`, data, nSamples, alleles)
}

bgenSampleIdsCpp <- function(ids, nSamples) {
  .Call(`_pecotmr_bgenSampleIdsCpp`, ids, nSamples)
}

dentistIterativeImpute <- function(ldMatR, nSample, zScoreR, pValueThreshold, propSVD, gcControl, nIter, gPvalueThreshold, numThreads, correctChenEtAlBug, verbose, seed) {
  .Call(`_pecotmr_dentistIterativeImpute`, ldMatR, nSample, zScoreR, pValueThreshold, propSVD, gcControl, nIter, gPvalueThreshold, numThreads, correctChenEtAlBug, verbose, seed)
}

dentistIterativeImputeFactor <- function(factorR, nSample, zScoreR, pValueThreshold, propSVD, gcControl, nIter, gPvalueThreshold, numThreads, correctChenEtAlBug, verbose, seed) {
  .Call(`_pecotmr_dentistIterativeImputeFactor`, factorR, nSample, zScoreR, pValueThreshold, propSVD, gcControl, nIter, gPvalueThreshold, numThreads, correctChenEtAlBug, verbose, seed)
}

lassosumRssCpp <- function(zR, LD, shrink, lambdaR, thr, maxiter) {
  .Call(`_pecotmr_lassosumRssCpp`, zR, LD, shrink, lambdaR, thr, maxiter)
}

lassosumRssFactorCpp <- function(zR, factorR, shrink, lambdaR, thr, maxiter) {
  .Call(`_pecotmr_lassosumRssFactorCpp`, zR, factorR, shrink, lambdaR, thr, maxiter)
}

ldThresholdComponents <- function(standardized, threshold, stripe) {
  .Call(`_pecotmr_ldThresholdComponents`, standardized, threshold, stripe)
}

penalizedRssCpp <- function(zR, LD, shrink, lambdaR, penaltyStr, gamma, alpha, lambda0, lambda2, thr, maxiter, maxSwaps) {
  .Call(`_pecotmr_penalizedRssCpp`, zR, LD, shrink, lambdaR, penaltyStr, gamma, alpha, lambda0, lambda2, thr, maxiter, maxSwaps)
}

penalizedRssFactorCpp <- function(zR, factorR, shrink, lambdaR, penaltyStr, gamma, alpha, lambda0, lambda2, thr, maxiter, maxSwaps) {
  .Call(`_pecotmr_penalizedRssFactorCpp`, zR, factorR, shrink, lambdaR, penaltyStr, gamma, alpha, lambda0, lambda2, thr, maxiter, maxSwaps)
}

prsCsCpp <- function(a, b, phi, bhat, maf, n, ldBlk, nIter, nBurnin, thin, verbose, seed) {
  .Call(`_pecotmr_prsCsCpp`, a, b, phi, bhat, maf, n, ldBlk, nIter, nBurnin, thin, verbose, seed)
}

prsCsFactorCpp <- function(a, b, phi, bhat, maf, n, factorR, nIter, nBurnin, thin, verbose, seed) {
  .Call(`_pecotmr_prsCsFactorCpp`, a, b, phi, bhat, maf, n, factorR, nIter, nBurnin, thin, verbose, seed)
}

qtlEnrichmentCpp <- function(rGwasPip, rQtlSusieFit, piGwas, piQtl, ImpN, shrinkageLambda, doubleShrinkage, besselCorrection, numThreads, seed) {
  .Call(`_pecotmr_qtlEnrichmentCpp`, rGwasPip, rQtlSusieFit, piGwas, piQtl, ImpN, shrinkageLambda, doubleShrinkage, besselCorrection, numThreads, seed)
}

sdprCpp <- function(bhatR, LD, n, perVariantSampleSize, array, a, c, M, a0k, b0k, iter, burn, thin, numThreads, optLlk, verbose, seed) {
  .Call(`_pecotmr_sdprCpp`, bhatR, LD, n, perVariantSampleSize, array, a, c, M, a0k, b0k, iter, burn, thin, numThreads, optLlk, verbose, seed)
}

sdprFactorCpp <- function(bhatR, factorR, n, perVariantSampleSize, array, a, c, M, a0k, b0k, iter, burn, thin, numThreads, optLlk, verbose, seed) {
  .Call(`_pecotmr_sdprFactorCpp`, bhatR, factorR, n, perVariantSampleSize, array, a, c, M, a0k, b0k, iter, burn, thin, numThreads, optLlk, verbose, seed)
}

vcfGtDosageCpp <- function(gt, alleles) {
  .Call(`_pecotmr_vcfGtDosageCpp`, gt, alleles)
}