R/RcppExports.R

In rqtl/qtl2geno: Treatment of Marker Genotypes for QTL Experiments

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

.calc_kinship <- function(prob_array) {
    .Call(`_qtl2geno_calc_kinship`, prob_array)
}

.crosstype_supported <- function(crosstype) {
    .Call(`_qtl2geno_crosstype_supported`, crosstype)
}

.count_invalid_genotypes <- function(crosstype, genotypes, is_X_chr, is_female, cross_info) {
    .Call(`_qtl2geno_count_invalid_genotypes`, crosstype, genotypes, is_X_chr, is_female, cross_info)
}

.check_crossinfo <- function(crosstype, cross_info, any_x_chr) {
    .Call(`_qtl2geno_check_crossinfo`, crosstype, cross_info, any_x_chr)
}

.check_is_female_vector <- function(crosstype, is_female, any_x_chr) {
    .Call(`_qtl2geno_check_is_female_vector`, crosstype, is_female, any_x_chr)
}

check_handle_x_chr <- function(crosstype, any_x_chr) {
    .Call(`_qtl2geno_check_handle_x_chr`, crosstype, any_x_chr)
}

.chisq_colpairs <- function(input) {
    .Call(`_qtl2geno_chisq_colpairs`, input)
}

.compare_geno <- function(geno) {
    .Call(`_qtl2geno_compare_geno`, geno)
}

.count_xo <- function(geno, crosstype, is_X_chr) {
    .Call(`_qtl2geno_count_xo`, geno, crosstype, is_X_chr)
}

.count_xo_3d <- function(geno_array, crosstype, is_X_chr) {
    .Call(`_qtl2geno_count_xo_3d`, geno_array, crosstype, is_X_chr)
}

mpp_encode_alleles <- function(allele1, allele2, n_alleles, phase_known) {
    .Call(`_qtl2geno_mpp_encode_alleles`, allele1, allele2, n_alleles, phase_known)
}

mpp_decode_geno <- function(true_gen, n_alleles, phase_known) {
    .Call(`_qtl2geno_mpp_decode_geno`, true_gen, n_alleles, phase_known)
}

mpp_is_het <- function(true_gen, n_alleles, phase_known) {
    .Call(`_qtl2geno_mpp_is_het`, true_gen, n_alleles, phase_known)
}

mpp_geno_names <- function(alleles, is_x_chr) {
    .Call(`_qtl2geno_mpp_geno_names`, alleles, is_x_chr)
}

invert_founder_index <- function(cross_info) {
    .Call(`_qtl2geno_invert_founder_index`, cross_info)
}

.is_phase_known <- function(crosstype) {
    .Call(`_qtl2geno_is_phase_known`, crosstype)
}

.find_ibd_segments <- function(g1, g2, p, error_prob) {
    .Call(`_qtl2geno_find_ibd_segments`, g1, g2, p, error_prob)
}

geno_names <- function(crosstype, alleles, is_x_chr) {
    .Call(`_qtl2geno_geno_names`, crosstype, alleles, is_x_chr)
}

nalleles <- function(crosstype) {
    .Call(`_qtl2geno_nalleles`, crosstype)
}

.genoprob_to_alleleprob <- function(crosstype, prob_array, is_x_chr) {
    .Call(`_qtl2geno_genoprob_to_alleleprob`, crosstype, prob_array, is_x_chr)
}

.get_x_covar <- function(crosstype, is_female, cross_info) {
    .Call(`_qtl2geno_get_x_covar`, crosstype, is_female, cross_info)
}

.guess_phase_f2A <- function(geno, deterministic) {
    .Call(`_qtl2geno_guess_phase_f2A`, geno, deterministic)
}

.guess_phase_f2X <- function(geno, deterministic) {
    .Call(`_qtl2geno_guess_phase_f2X`, geno, deterministic)
}

.guess_phase_A <- function(geno, crosstype, deterministic) {
    .Call(`_qtl2geno_guess_phase_A`, geno, crosstype, deterministic)
}

.guess_phase_X <- function(geno, crosstype, is_female, deterministic) {
    .Call(`_qtl2geno_guess_phase_X`, geno, crosstype, is_female, deterministic)
}

.calc_errorlod <- function(crosstype, probs, genotypes, founder_geno, is_X_chr, is_female, cross_info) {
    .Call(`_qtl2geno_calc_errorlod`, crosstype, probs, genotypes, founder_geno, is_X_chr, is_female, cross_info)
}

.calc_genoprob <- function(crosstype, genotypes, founder_geno, is_X_chr, is_female, cross_info, rec_frac, marker_index, error_prob) {
    .Call(`_qtl2geno_calc_genoprob`, crosstype, genotypes, founder_geno, is_X_chr, is_female, cross_info, rec_frac, marker_index, error_prob)
}

.calc_genoprob2 <- function(crosstype, genotypes, founder_geno, is_X_chr, is_female, cross_info, rec_frac, marker_index, error_prob) {
    .Call(`_qtl2geno_calc_genoprob2`, 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(`_qtl2geno_est_map`, crosstype, genotypes, founder_geno, is_X_chr, is_female, cross_info, rec_frac, error_prob, max_iterations, tol, verbose)
}

.est_map2 <- function(crosstype, genotypes, founder_geno, is_X_chr, is_female, cross_info, cross_group, unique_cross_group, rec_frac, error_prob, max_iterations, tol, verbose) {
    .Call(`_qtl2geno_est_map2`, crosstype, genotypes, founder_geno, is_X_chr, is_female, cross_info, cross_group, unique_cross_group, rec_frac, error_prob, max_iterations, tol, verbose)
}

.sim_geno <- function(crosstype, genotypes, founder_geno, is_X_chr, is_female, cross_info, rec_frac, marker_index, error_prob, n_draws) {
    .Call(`_qtl2geno_sim_geno`, crosstype, genotypes, founder_geno, is_X_chr, is_female, cross_info, rec_frac, marker_index, error_prob, n_draws)
}

.sim_geno2 <- function(crosstype, genotypes, founder_geno, is_X_chr, is_female, cross_info, rec_frac, marker_index, error_prob, n_draws) {
    .Call(`_qtl2geno_sim_geno2`, crosstype, genotypes, founder_geno, is_X_chr, is_female, cross_info, rec_frac, marker_index, error_prob, n_draws)
}

addlog <- function(a, b) {
    .Call(`_qtl2geno_addlog`, a, b)
}

subtrlog <- function(a, b) {
    .Call(`_qtl2geno_subtrlog`, a, b)
}

.viterbi <- function(crosstype, genotypes, founder_geno, is_X_chr, is_female, cross_info, rec_frac, marker_index, error_prob) {
    .Call(`_qtl2geno_viterbi`, crosstype, genotypes, founder_geno, is_X_chr, is_female, cross_info, rec_frac, marker_index, error_prob)
}

.viterbi2 <- function(crosstype, genotypes, founder_geno, is_X_chr, is_female, cross_info, rec_frac, marker_index, error_prob) {
    .Call(`_qtl2geno_viterbi2`, crosstype, genotypes, founder_geno, is_X_chr, is_female, cross_info, rec_frac, marker_index, error_prob)
}

.interp_genoprob_onechr <- function(genoprob, map, pos_index) {
    .Call(`_qtl2geno_interp_genoprob_onechr`, genoprob, map, pos_index)
}

.locate_xo <- function(geno, map, crosstype, is_X_chr) {
    .Call(`_qtl2geno_locate_xo`, geno, map, crosstype, is_X_chr)
}

.maxmarg <- function(prob_array, minprob, tol) {
    .Call(`_qtl2geno_maxmarg`, prob_array, minprob, tol)
}

.reduce_markers <- function(pos, weights, min_dist) {
    .Call(`_qtl2geno_reduce_markers`, pos, weights, min_dist)
}

test_init <- function(crosstype, true_gen, is_x_chr, is_female, cross_info) {
    .Call(`_qtl2geno_test_init`, 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(`_qtl2geno_test_emit`, 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(`_qtl2geno_test_step`, 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(`_qtl2geno_test_check_geno`, 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(`_qtl2geno_test_possible_gen`, crosstype, is_x_chr, is_female, cross_info)
}

test_ngen <- function(crosstype, is_x_chr) {
    .Call(`_qtl2geno_test_ngen`, crosstype, is_x_chr)
}

test_nrec <- function(crosstype, gen_left, gen_right, is_x_chr, is_female, cross_info) {
    .Call(`_qtl2geno_test_nrec`, crosstype, gen_left, gen_right, is_x_chr, is_female, cross_info)
}

test_founder_geno_values <- function(crosstype, founder_geno) {
    .Call(`_qtl2geno_test_founder_geno_values`, crosstype, founder_geno)
}

need_founder_geno <- function(crosstype) {
    .Call(`_qtl2geno_need_founder_geno`, crosstype)
}

check_founder_geno_size <- function(crosstype, founder_geno, n_markers) {
    .Call(`_qtl2geno_check_founder_geno_size`, crosstype, founder_geno, n_markers)
}

test_emitmatrix <- function(crosstype, error_prob, max_obsgeno, founder_geno, is_x_chr, is_female, cross_info) {
    .Call(`_qtl2geno_test_emitmatrix`, crosstype, error_prob, max_obsgeno, founder_geno, is_x_chr, is_female, cross_info)
}

test_stepmatrix <- function(crosstype, rec_frac, is_x_chr, is_female, cross_info) {
    .Call(`_qtl2geno_test_stepmatrix`, crosstype, rec_frac, is_x_chr, is_female, cross_info)
}

test_initvector <- function(crosstype, is_x_chr, is_female, cross_info) {
    .Call(`_qtl2geno_test_initvector`, crosstype, is_x_chr, is_female, cross_info)
}