scran_norm
Scaling normalization of single-cell data
Loading...
Searching...
No Matches
choose_pseudo_count.hpp
Go to the documentation of this file.
1#ifndef SCRAN_NORM_CHOOSE_PSEUDO_COUNT_HPP
2#define SCRAN_NORM_CHOOSE_PSEUDO_COUNT_HPP
3
4#include <algorithm>
5#include <vector>
6#include <cstddef>
7
13namespace scran_norm {
14
24 double quantile = 0.05;
25
29 double max_bias = 0.1;
30
35 double min_value = 1;
36};
37
41namespace internal {
42
43template<typename Float_>
44Float_ find_quantile(Float_ quantile, std::size_t n, Float_* ptr) {
45 double raw = static_cast<double>(n - 1) * quantile;
46 std::size_t index = std::ceil(raw);
47 std::nth_element(ptr, ptr + index, ptr + n);
48 double upper = *(ptr + index);
49 std::nth_element(ptr, ptr + index - 1, ptr + index);
50 double lower = *(ptr + index - 1);
51 return lower * (index - raw) + upper * (raw - (index - 1));
52}
53
54}
87template<typename Float_>
88Float_ choose_pseudo_count_raw(std::size_t num, Float_* size_factors, const ChoosePseudoCountOptions& options) {
89 if (num <= 1) {
90 return options.min_value;
91 }
92
93 // Avoid problems with zeros.
94 decltype(num) counter = 0;
95 for (decltype(num) i = 0; i < num; ++i) {
96 auto val = size_factors[i];
97 if (std::isfinite(val) && val > 0) {
98 if (i != counter) {
99 size_factors[counter] = val;
100 }
101 ++counter;
102 }
103 }
104 num = counter;
105
106 if (num <= 1) {
107 return options.min_value;
108 }
109
110 double lower_sf, upper_sf;
111 if (options.quantile == 0) {
112 lower_sf = *std::min_element(size_factors, size_factors + num);
113 upper_sf = *std::max_element(size_factors, size_factors + num);
114 } else {
115 lower_sf = internal::find_quantile(options.quantile, num, size_factors);
116 upper_sf = internal::find_quantile(1 - options.quantile, num, size_factors);
117 }
118
119 // Very confusing formulation in Equation 3, but whatever.
120 Float_ pseudo_count = (1.0 / lower_sf - 1.0 / upper_sf) / (8 * options.max_bias);
121
122 return std::max(options.min_value, pseudo_count);
123}
124
135template<typename Float_>
136Float_ choose_pseudo_count(std::size_t num, const Float_* size_factors, const ChoosePseudoCountOptions& options) {
137 std::vector<Float_> buffer(size_factors, size_factors + num);
138 return choose_pseudo_count_raw(num, buffer.data(), options);
139}
140
141}
142
143#endif
Scaling normalization of single-cell data.
Definition center_size_factors.hpp:19
Float_ choose_pseudo_count_raw(std::size_t num, Float_ *size_factors, const ChoosePseudoCountOptions &options)
Definition choose_pseudo_count.hpp:88
Float_ choose_pseudo_count(std::size_t num, const Float_ *size_factors, const ChoosePseudoCountOptions &options)
Definition choose_pseudo_count.hpp:136
Options for choose_pseudo_count().
Definition choose_pseudo_count.hpp:18
double quantile
Definition choose_pseudo_count.hpp:24
double max_bias
Definition choose_pseudo_count.hpp:29
double min_value
Definition choose_pseudo_count.hpp:35