R/RcppExports.R

In simecek/qtl2: Tools for analyzing high-dimensional QTL experiments

# This file was generated by Rcpp::compileAttributes
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

.calc_genetic_sim <- function(prob_array) {
    .Call('qtl2_calc_genetic_sim', PACKAGE = 'qtl2', prob_array)
}

.crosstype_supported <- function(crosstype) {
    .Call('qtl2_crosstype_supported', PACKAGE = 'qtl2', crosstype)
}

.count_invalid_genotypes <- function(crosstype, genotypes, is_X_chr, is_female, cross_info) {
    .Call('qtl2_count_invalid_genotypes', PACKAGE = 'qtl2', crosstype, genotypes, is_X_chr, is_female, cross_info)
}

check_crossinfo <- function(crosstype, cross_info, any_x_chr) {
    .Call('qtl2_check_crossinfo', PACKAGE = 'qtl2', crosstype, cross_info, any_x_chr)
}

check_is_female_vector <- function(crosstype, is_female, any_x_chr) {
    .Call('qtl2_check_is_female_vector', PACKAGE = 'qtl2', crosstype, is_female, any_x_chr)
}

check_handle_x_chr <- function(crosstype, any_x_chr) {
    .Call('qtl2_check_handle_x_chr', PACKAGE = 'qtl2', crosstype, any_x_chr)
}

.genoprob_to_alleleprob <- function(crosstype, prob_array, is_x_chr) {
    .Call('qtl2_genoprob_to_alleleprob', PACKAGE = 'qtl2', crosstype, prob_array, is_x_chr)
}

.calc_genoprob <- function(crosstype, genotypes, founder_geno, is_X_chr, is_female, cross_info, rec_frac, marker_index, error_prob) {
    .Call('qtl2_calc_genoprob', PACKAGE = 'qtl2', crosstype, genotypes, founder_geno, is_X_chr, is_female, cross_info, rec_frac, marker_index, error_prob)
}

.est_map <- function(crosstype, genotypes, founder_geno, is_X_chr, is_female, cross_info, rec_frac, error_prob, max_iterations, tol, verbose) {
    .Call('qtl2_est_map', PACKAGE = 'qtl2', crosstype, genotypes, founder_geno, is_X_chr, is_female, cross_info, rec_frac, error_prob, max_iterations, tol, verbose)
}

addlog <- function(a, b) {
    .Call('qtl2_addlog', PACKAGE = 'qtl2', a, b)
}

interpolate_map <- function(oldpos, oldmap, newmap) {
    .Call('qtl2_interpolate_map', PACKAGE = 'qtl2', oldpos, oldmap, newmap)
}

fit_linreg_eigenchol <- function(X, y) {
    .Call('qtl2_fit_linreg_eigenchol', PACKAGE = 'qtl2', X, y)
}

calc_rss_eigenchol <- function(X, y) {
    .Call('qtl2_calc_rss_eigenchol', PACKAGE = 'qtl2', X, y)
}

fit_linreg_eigenqr <- function(X, y) {
    .Call('qtl2_fit_linreg_eigenqr', PACKAGE = 'qtl2', X, y)
}

calc_rss_eigenqr <- function(X, y) {
    .Call('qtl2_calc_rss_eigenqr', PACKAGE = 'qtl2', X, y)
}

calc_mvrss_eigenchol <- function(X, Y) {
    .Call('qtl2_calc_mvrss_eigenchol', PACKAGE = 'qtl2', X, Y)
}

calc_mvrss_eigenqr <- function(X, Y) {
    .Call('qtl2_calc_mvrss_eigenqr', PACKAGE = 'qtl2', X, Y)
}

calc_rss_lapack <- function(X, Y, skip_dgels = FALSE, tol = 1e-10) {
    .Call('qtl2_calc_rss_lapack', PACKAGE = 'qtl2', X, Y, skip_dgels, tol)
}

cbind_imatrix <- function(mat1, mat2) {
    .Call('qtl2_cbind_imatrix', PACKAGE = 'qtl2', mat1, mat2)
}

cbind_3imatrix <- function(mat1, mat2, mat3) {
    .Call('qtl2_cbind_3imatrix', PACKAGE = 'qtl2', mat1, mat2, mat3)
}

cbind_nmatrix <- function(mat1, mat2) {
    .Call('qtl2_cbind_nmatrix', PACKAGE = 'qtl2', mat1, mat2)
}

cbind_3nmatrix <- function(mat1, mat2, mat3) {
    .Call('qtl2_cbind_3nmatrix', PACKAGE = 'qtl2', mat1, mat2, mat3)
}

rbind_imatrix <- function(mat1, mat2) {
    .Call('qtl2_rbind_imatrix', PACKAGE = 'qtl2', mat1, mat2)
}

rbind_3imatrix <- function(mat1, mat2, mat3) {
    .Call('qtl2_rbind_3imatrix', PACKAGE = 'qtl2', mat1, mat2, mat3)
}

rbind_nmatrix <- function(mat1, mat2) {
    .Call('qtl2_rbind_nmatrix', PACKAGE = 'qtl2', mat1, mat2)
}

rbind_3nmatrix <- function(mat1, mat2, mat3) {
    .Call('qtl2_rbind_3nmatrix', PACKAGE = 'qtl2', mat1, mat2, mat3)
}

random_int <- function(n, low, high) {
    .Call('qtl2_random_int', PACKAGE = 'qtl2', n, low, high)
}

get_permutation <- function(n) {
    .Call('qtl2_get_permutation', PACKAGE = 'qtl2', n)
}

permute_nvector <- function(n_perm, x) {
    .Call('qtl2_permute_nvector', PACKAGE = 'qtl2', n_perm, x)
}

permute_ivector <- function(n_perm, x) {
    .Call('qtl2_permute_ivector', PACKAGE = 'qtl2', n_perm, x)
}

permute_nvector_stratified <- function(n_perm, x, strata, n_strata = -1L) {
    .Call('qtl2_permute_nvector_stratified', PACKAGE = 'qtl2', n_perm, x, strata, n_strata)
}

permute_ivector_stratified <- function(n_perm, x, strata, n_strata = -1L) {
    .Call('qtl2_permute_ivector_stratified', PACKAGE = 'qtl2', n_perm, x, strata, n_strata)
}

test_init <- function(crosstype, true_gen, is_x_chr, is_female, cross_info) {
    .Call('qtl2_test_init', PACKAGE = 'qtl2', crosstype, true_gen, is_x_chr, is_female, cross_info)
}

test_emit <- function(crosstype, obs_gen, true_gen, error_prob, founder_geno, is_x_chr, is_female, cross_info) {
    .Call('qtl2_test_emit', PACKAGE = 'qtl2', crosstype, obs_gen, true_gen, error_prob, founder_geno, is_x_chr, is_female, cross_info)
}

test_step <- function(crosstype, gen_left, gen_right, rec_frac, is_x_chr, is_female, cross_info) {
    .Call('qtl2_test_step', PACKAGE = 'qtl2', crosstype, gen_left, gen_right, rec_frac, is_x_chr, is_female, cross_info)
}

test_check_geno <- function(crosstype, gen, is_observed_value, is_x_chr, is_female, cross_info) {
    .Call('qtl2_test_check_geno', PACKAGE = 'qtl2', crosstype, gen, is_observed_value, is_x_chr, is_female, cross_info)
}

test_possible_gen <- function(crosstype, is_x_chr, is_female, cross_info) {
    .Call('qtl2_test_possible_gen', PACKAGE = 'qtl2', crosstype, is_x_chr, is_female, cross_info)
}

test_ngen <- function(crosstype, is_x_chr) {
    .Call('qtl2_test_ngen', PACKAGE = 'qtl2', crosstype, is_x_chr)
}

test_nrec <- function(crosstype, gen_left, gen_right, is_x_chr, is_female, cross_info) {
    .Call('qtl2_test_nrec', PACKAGE = 'qtl2', crosstype, gen_left, gen_right, is_x_chr, is_female, cross_info)
}