R/RcppExports.R

In gpart: Human genome partitioning of dense sequencing data by identifying haplotype blocks

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

VCFtogeno <- function(vcf) {
    .Call(`_gpart_VCFtogeno`, vcf)
}

pairCubeX <- function(b1, b2) {
    .Call(`_gpart_pairCubeX`, b1, b2)
}

matCubeX <- function(geno) {
    .Call(`_gpart_matCubeX`, geno)
}

matCubeX2 <- function(geno1, geno2) {
    .Call(`_gpart_matCubeX2`, geno1, geno2)
}

estiD <- function(pA, pB, n11, n12, n21, n22, n1212) {
    .Call(`_gpart_estiD`, pA, pB, n11, n12, n21, n22, n1212)
}

CIDp <- function(b1, b2) {
    .Call(`_gpart_CIDp`, b1, b2)
}

genoDp <- function(geno, strLD = TRUE, lower = 0.7, upper = 0.98) {
    .Call(`_gpart_genoDp`, geno, strLD, lower, upper)
}

genoCubeDp <- function(geno) {
    .Call(`_gpart_genoCubeDp`, geno)
}

genoDp2 <- function(geno1, geno2, strLD = TRUE, lower = 0.7, upper = 0.98) {
    .Call(`_gpart_genoDp2`, geno1, geno2, strLD, lower, upper)
}

calc_lnlike <- function(known11, known12, known21, known22, center_ct_d, freq11, freq12, freq21, freq22, half_hethet_share, freq11_incr) {
    .Call(`_gpart_calc_lnlike`, known11, known12, known21, known22, center_ct_d, freq11, freq12, freq21, freq22, half_hethet_share, freq11_incr)
}

cubic_real_roots <- function(coef_a, coef_b, coef_c, solutions) {
    .Call(`_gpart_cubic_real_roots`, coef_a, coef_b, coef_c, solutions)
}

calc_lnlike_quantile <- function(known11, known12, known21, known22, unknown_dh, freqx1, freq1x, freq2x, freq11_expected, denom, quantile) {
    .Call(`_gpart_calc_lnlike_quantile`, known11, known12, known21, known22, unknown_dh, freqx1, freq1x, freq2x, freq11_expected, denom, quantile)
}

em_phase_hethet <- function(known11, known12, known21, known22, center_ct, onside_sol_ct_ptr) {
    .Call(`_gpart_em_phase_hethet`, known11, known12, known21, known22, center_ct, onside_sol_ct_ptr)
}

haploview_blocks_classify <- function(counts, lowci_max, lowci_min, recomb_highci, strong_highci, strong_lowci, strong_lowci_outer, is_x, recomb_fast_ln_thresh) {
    .Call(`_gpart_haploview_blocks_classify`, counts, lowci_max, lowci_min, recomb_highci, strong_highci, strong_lowci, strong_lowci_outer, is_x, recomb_fast_ln_thresh)
}

CIDp_strLD <- function(b1, b2, lower, upper) {
    .Call(`_gpart_CIDp_strLD`, b1, b2, lower, upper)
}