# Generated by using Rcpp::compileAttributes() -> do not edit by hand
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
#' Calculate the constant theta, given `m`
#'
#' `calc_theta` is used to calculate the shrinkage coefficient used by LDshrink
#'
#' @param m a number indicating the size of the panel used to create the
NULL
#' @export
calc_theta <- function(m) {
.Call(`_ldshrink_calc_theta_exp`, m)
}
shrinkCov <- function(S, mapd, m, Ne, cutoff) {
.Call(`_ldshrink_shrinkCov`, S, mapd, m, Ne, cutoff)
}
fastldshrink <- function(genotype_data, mapd, m, Ne, cutoff, isGeno = TRUE, cov_2_cor = TRUE) {
.Call(`_ldshrink_fastldshrink`, genotype_data, mapd, m, Ne, cutoff, isGeno, cov_2_cor)
}
calcDist <- function(map) {
.Call(`_ldshrink_calcDist`, map)
}
sparse_ldshrink <- function(data, mapd, indices, m, Ne, cutoff, total_size, progress = TRUE, useldshrink = TRUE) {
.Call(`_ldshrink_sparse_ldshrink`, data, mapd, indices, m, Ne, cutoff, total_size, progress, useldshrink)
}
sparse_ldshrink_p <- function(data_a, data_b, mapd_a, mapd_b, indices_a, indices_b, m, Ne, cutoff, total_size, progress = FALSE, useldshrink = TRUE) {
.Call(`_ldshrink_sparse_ldshrink_p`, data_a, data_b, mapd_a, mapd_b, indices_a, indices_b, m, Ne, cutoff, total_size, progress, useldshrink)
}
ld2df <- function(data, mapd, rsid, m, Ne, cutoff, r2cutoff = 0.01, progress = FALSE, useldshrink = TRUE) {
.Call(`_ldshrink_ld2df`, data, mapd, rsid, m, Ne, cutoff, r2cutoff, progress, useldshrink)
}
ld2df_p <- function(data_a, data_b, mapd_a, mapd_b, rsid_a, rsid_b, m, Ne, cutoff, r2cutoff = 0.01, progress = FALSE, useldshrink = TRUE) {
.Call(`_ldshrink_ld2df_p`, data_a, data_b, mapd_a, mapd_b, rsid_a, rsid_b, m, Ne, cutoff, r2cutoff, progress, useldshrink)
}
flip_allele <- function(gwas_ref, gwas_alt, ld_ref, ld_alt) {
.Call(`_ldshrink_flip_allele`, gwas_ref, gwas_alt, ld_ref, ld_alt)
}
sorted_snp_df <- function(snp_info) {
.Call(`_ldshrink_sorted_snp_df`, snp_info)
}
set_ld_region <- function(ld_regions, snp_info, assign_all = TRUE) {
.Call(`_ldshrink_set_ld_region`, ld_regions, snp_info, assign_all)
}
interpolate_map <- function(map, map_pos, target_pos, progress = FALSE) {
.Call(`_ldshrink_interpolate_map`, map, map_pos, target_pos, progress)
}
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