choose_highly_variable_genes.hpp

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#ifndef SCRAN_VARIANCES_CHOOSE_HIGHLY_VARIABLE_GENES_HPP
#define SCRAN_VARIANCES_CHOOSE_HIGHLY_VARIABLE_GENES_HPP
 
#include <vector>
#include <algorithm>
#include <numeric>
#include <cstddef>
 
#include "sanisizer/sanisizer.hpp"
#include "topicks/topicks.hpp"
 
namespace scran_variances {
 
struct ChooseHighlyVariableGenesOptions {
    std::size_t top = 4000;
 
    bool larger = true;
 
    bool use_bound = false;
 
    double bound = 0;
 
    bool keep_ties = true;
};
 
namespace internal {
 
template<typename Stat_>
topicks::PickTopGenesOptions<Stat_> translate_options(const ChooseHighlyVariableGenesOptions& chvg_options) {
    topicks::PickTopGenesOptions<Stat_> opt;
    opt.keep_ties = chvg_options.keep_ties;
    if (chvg_options.use_bound) {
        opt.bound = chvg_options.bound;
    }
    return opt;
}
 
}
template<typename Stat_, typename Bool_>
void choose_highly_variable_genes(std::size_t n, const Stat_* statistic, Bool_* output, const ChooseHighlyVariableGenesOptions& options) {
    topicks::pick_top_genes(n, statistic, options.top, options.larger, output, internal::translate_options<Stat_>(options));
}
 
template<typename Bool_ = char, typename Stat_>
std::vector<Bool_> choose_highly_variable_genes(std::size_t n, const Stat_* statistic, const ChooseHighlyVariableGenesOptions& options) {
    auto output = sanisizer::create<std::vector<Bool_> >(n
#ifdef SCRAN_VARIANCES_TEST_INIT
        , SCRAN_VARIANCES_TEST_INIT
#endif
    );
    choose_highly_variable_genes(n, statistic, output.data(), options);
    return output;
}
 
template<typename Index_, typename Stat_>
std::vector<Index_> choose_highly_variable_genes_index(Index_ n, const Stat_* statistic, const ChooseHighlyVariableGenesOptions& options) {
    return topicks::pick_top_genes_index<Index_>(n, statistic, options.top, options.larger, internal::translate_options<Stat_>(options));
}
 
}
 
#endif