R/RcppExports.R

In xihaoli/STAAR: STAAR Procedure for Dynamic Incorporation of Multiple Functional Annotations in Whole-Genome Sequencing Studies

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

Bisection <- function(egvalues, q, xmin, xmax) {
    .Call(`_STAAR_Bisection`, egvalues, q, xmin, xmax)
}

Bisection_Binary_SPA <- function(muhat, G, q, xmin, xmax, tol) {
    .Call(`_STAAR_Bisection_Binary_SPA`, muhat, G, q, xmin, xmax, tol)
}

CCT_pval <- function(x, weights) {
    .Call(`_STAAR_CCT_pval`, x, weights)
}

Indiv_Score_Test <- function(G, X, working, sigma, fam, residuals) {
    .Call(`_STAAR_Indiv_Score_Test`, G, X, working, sigma, fam, residuals)
}

Indiv_Score_Test_SMMAT <- function(G, P, residuals) {
    .Call(`_STAAR_Indiv_Score_Test_SMMAT`, G, P, residuals)
}

Indiv_Score_Test_SMMAT_sparse <- function(G, Sigma_i, Sigma_iX, cov, residuals) {
    .Call(`_STAAR_Indiv_Score_Test_SMMAT_sparse`, G, Sigma_i, Sigma_iX, cov, residuals)
}

Indiv_Score_Test_SMMAT_sparse_cond <- function(G, Sigma_i, Sigma_iX, cov, X_adj, residuals) {
    .Call(`_STAAR_Indiv_Score_Test_SMMAT_sparse_cond`, G, Sigma_i, Sigma_iX, cov, X_adj, residuals)
}

K <- function(x, egvalues) {
    .Call(`_STAAR_K`, x, egvalues)
}

K1 <- function(x, egvalues, q) {
    .Call(`_STAAR_K1`, x, egvalues, q)
}

K1_Binary_SPA <- function(x, muhat, G, q) {
    .Call(`_STAAR_K1_Binary_SPA`, x, muhat, G, q)
}

K1_Binary_SPA_alt <- function(x, muhat, G, q) {
    .Call(`_STAAR_K1_Binary_SPA_alt`, x, muhat, G, q)
}

K2 <- function(x, egvalues) {
    .Call(`_STAAR_K2`, x, egvalues)
}

K2_Binary_SPA <- function(x, muhat, G) {
    .Call(`_STAAR_K2_Binary_SPA`, x, muhat, G)
}

K2_Binary_SPA_alt <- function(x, muhat, G) {
    .Call(`_STAAR_K2_Binary_SPA_alt`, x, muhat, G)
}

K_Binary_SPA <- function(x, muhat, G) {
    .Call(`_STAAR_K_Binary_SPA`, x, muhat, G)
}

K_Binary_SPA_alt <- function(x, muhat, G) {
    .Call(`_STAAR_K_Binary_SPA_alt`, x, muhat, G)
}

NR_Binary_SPA <- function(muhat, G, q, init, tol, max_iter) {
    .Call(`_STAAR_NR_Binary_SPA`, muhat, G, q, init, tol, max_iter)
}

STAAR_B_Binary_SPA <- function(G, XW, XXWX_inv, residuals, muhat, weights_B, tol, max_iter) {
    .Call(`_STAAR_STAAR_B_Binary_SPA`, G, XW, XXWX_inv, residuals, muhat, weights_B, tol, max_iter)
}

STAAR_B_SPA <- function(G, XW, XXWX_inv, residuals, muhat, weights_B, tol, max_iter, p_filter_cutoff, G_sp, X, working, sigma, fam) {
    .Call(`_STAAR_STAAR_B_SPA`, G, XW, XXWX_inv, residuals, muhat, weights_B, tol, max_iter, p_filter_cutoff, G_sp, X, working, sigma, fam)
}

STAAR_B_SPA_SMMAT <- function(G, XW, XXWX_inv, residuals, muhat, weights_B, tol, max_iter, p_filter_cutoff, G_sp, P) {
    .Call(`_STAAR_STAAR_B_SPA_SMMAT`, G, XW, XXWX_inv, residuals, muhat, weights_B, tol, max_iter, p_filter_cutoff, G_sp, P)
}

STAAR_B_SPA_SMMAT_sparse <- function(G, XW, XXWX_inv, residuals, muhat, weights_B, tol, max_iter, p_filter_cutoff, G_sp, Sigma_i, Sigma_iX, cov) {
    .Call(`_STAAR_STAAR_B_SPA_SMMAT_sparse`, G, XW, XXWX_inv, residuals, muhat, weights_B, tol, max_iter, p_filter_cutoff, G_sp, Sigma_i, Sigma_iX, cov)
}

STAAR_O <- function(G, X, working, sigma, fam, residuals, weights_B, weights_S, weights_A, mac, mac_thres = 10L) {
    .Call(`_STAAR_STAAR_O`, G, X, working, sigma, fam, residuals, weights_B, weights_S, weights_A, mac, mac_thres)
}

STAAR_O_SMMAT <- function(G, P, residuals, weights_B, weights_S, weights_A, mac, mac_thres = 10L) {
    .Call(`_STAAR_STAAR_O_SMMAT`, G, P, residuals, weights_B, weights_S, weights_A, mac, mac_thres)
}

STAAR_O_SMMAT_sparse <- function(G, Sigma_i, Sigma_iX, cov, residuals, weights_B, weights_S, weights_A, mac, mac_thres = 10L) {
    .Call(`_STAAR_STAAR_O_SMMAT_sparse`, G, Sigma_i, Sigma_iX, cov, residuals, weights_B, weights_S, weights_A, mac, mac_thres)
}

STAAR_O_SMMAT_sparse_cond <- function(G, Sigma_i, Sigma_iX, cov, X_adj, residuals, weights_B, weights_S, weights_A, mac, mac_thres = 10L) {
    .Call(`_STAAR_STAAR_O_SMMAT_sparse_cond`, G, Sigma_i, Sigma_iX, cov, X_adj, residuals, weights_B, weights_S, weights_A, mac, mac_thres)
}

Saddle <- function(q, egvalues) {
    .Call(`_STAAR_Saddle`, q, egvalues)
}

Saddle_Binary_SPA <- function(q, muhat, G, tol, max_iter, lower) {
    .Call(`_STAAR_Saddle_Binary_SPA`, q, muhat, G, tol, max_iter, lower)
}

Saddle_Binary_SPA_Bisection <- function(q, muhat, G, tol, max_iter, xmin, xmax, lower) {
    .Call(`_STAAR_Saddle_Binary_SPA_Bisection`, q, muhat, G, tol, max_iter, xmin, xmax, lower)
}

check_is_na <- function(x) {
    .Call(`_STAAR_check_is_na`, x)
}

goldenSectionSearchForSignChange <- function(a, b, muhat, G, q, tol, max_iter) {
    .Call(`_STAAR_goldenSectionSearchForSignChange`, a, b, muhat, G, q, tol, max_iter)
}

haveSameSign <- function(a, b) {
    .Call(`_STAAR_haveSameSign`, a, b)
}

matrix_flip <- function(G) {
    .Call(`_STAAR_matrix_flip`, G)
}

matrix_impute <- function(G) {
    .Call(`_STAAR_matrix_impute`, G)
}

# Register entry points for exported C++ functions
methods::setLoadAction(function(ns) {
    .Call('_STAAR_RcppExport_registerCCallable', PACKAGE = 'STAAR')
})