1#ifndef SCRAN_NORM_CHOOSE_PSEUDO_COUNT_HPP
2#define SCRAN_NORM_CHOOSE_PSEUDO_COUNT_HPP
46template<
typename Float_>
47Float_ find_quantile(Float_ quantile, std::size_t n, Float_* ptr) {
48 double raw =
static_cast<double>(n - 1) * quantile;
49 std::size_t index = std::ceil(raw);
50 std::nth_element(ptr, ptr + index, ptr + n);
51 double upper = *(ptr + index);
52 std::nth_element(ptr, ptr + index - 1, ptr + index);
53 double lower = *(ptr + index - 1);
54 return lower * (index - raw) + upper * (raw - (index - 1));
96template<
typename Float_>
103 decltype(I(num)) counter = 0;
104 for (
decltype(I(num)) i = 0; i < num; ++i) {
105 const auto val = size_factors[i];
106 if (std::isfinite(val) && val > 0) {
108 size_factors[counter] = val;
119 Float_ lower_sf, upper_sf;
121 lower_sf = *std::min_element(size_factors, size_factors + num);
122 upper_sf = *std::max_element(size_factors, size_factors + num);
124 lower_sf = internal::find_quantile(options.
quantile, num, size_factors);
125 upper_sf = internal::find_quantile(1 - options.
quantile, num, size_factors);
129 const Float_ pseudo_count = (1.0 / lower_sf - 1.0 / upper_sf) / (8 * options.
max_bias);
131 return std::max(options.
min_value, pseudo_count);
146template<
typename Float_>
148 std::vector<Float_> buffer(size_factors, size_factors + num);
Scaling normalization of single-cell data.
Definition center_size_factors.hpp:20
Float_ choose_pseudo_count(const std::size_t num, const Float_ *const size_factors, const ChoosePseudoCountOptions &options)
Definition choose_pseudo_count.hpp:147
Float_ choose_pseudo_count_raw(std::size_t num, Float_ *const size_factors, const ChoosePseudoCountOptions &options)
Definition choose_pseudo_count.hpp:97
Options for choose_pseudo_count().
Definition choose_pseudo_count.hpp:20
double quantile
Definition choose_pseudo_count.hpp:26
double max_bias
Definition choose_pseudo_count.hpp:32
double min_value
Definition choose_pseudo_count.hpp:38