jade::basic_neoscan< TValue > Class Template Reference

A template for a class implementing the neoscan algorithm. This algorithm scans for positive selection between ancient and modern data. It can take advantage of the dating for each individual ancient sample. More...

#include <jade.neoscan.hpp>

Collaboration diagram for jade::basic_neoscan< TValue >:

Data Structures
struct	output
	Output for one column. More...

Public Types
typedef TValue	value_type
	The value type. More...
typedef basic_matrix< value_type >	matrix_type
	The matrix type. More...
typedef basic_verification< value_type >	verification_type
	The verification type. More...
typedef basic_genotype_matrix< value_type >	genotype_matrix_type
	The genotype matrix type. More...
typedef basic_genotype_matrix_factory< value_type >	genotype_matrix_factory_type
	The genotype matrix factory type. More...

Public Member Functions
	basic_neoscan (const genotype_matrix_type &g, const matrix_type &q, const matrix_type &f, const matrix_type &years)
	Initializes a new instance of the class. Memory for the specified G, Q, and Fa matrices must remain valid for the lifetime of this instance. More...
template<typename TOutputAction >
void	execute (const TOutputAction &output_action) const
	Executes the algorithm using the specified action for the output of each column. More...

Static Public Member Functions
static void	run (args &a)
	Runs the program based on command-line arguments. More...

Detailed Description

template<typename TValue>
class jade::basic_neoscan< TValue >

A template for a class implementing the neoscan algorithm. This algorithm scans for positive selection between ancient and modern data. It can take advantage of the dating for each individual ancient sample.

Definition at line 21 of file jade.neoscan.hpp.

Member Typedef Documentation

genotype_matrix_factory_type

template<typename TValue >

typedef basic_genotype_matrix_factory<value_type> jade::basic_neoscan< TValue >::genotype_matrix_factory_type

The genotype matrix factory type.

Definition at line 43 of file jade.neoscan.hpp.

genotype_matrix_type

template<typename TValue >

typedef basic_genotype_matrix<value_type> jade::basic_neoscan< TValue >::genotype_matrix_type

The genotype matrix type.

Definition at line 38 of file jade.neoscan.hpp.

matrix_type

template<typename TValue >

typedef basic_matrix<value_type> jade::basic_neoscan< TValue >::matrix_type

The matrix type.

Definition at line 32 of file jade.neoscan.hpp.

value_type

template<typename TValue >

typedef TValue jade::basic_neoscan< TValue >::value_type

The value type.

Definition at line 29 of file jade.neoscan.hpp.

verification_type

template<typename TValue >

typedef basic_verification<value_type> jade::basic_neoscan< TValue >::verification_type

The verification type.

Definition at line 35 of file jade.neoscan.hpp.

Constructor & Destructor Documentation

basic_neoscan()

template<typename TValue >

jade::basic_neoscan< TValue >::basic_neoscan ( const genotype_matrix_type &  g, const matrix_type &  q, const matrix_type &  f, const matrix_type &  years  )

inline

Initializes a new instance of the class. Memory for the specified G, Q, and Fa matrices must remain valid for the lifetime of this instance.

Parameters

g	The G matrix.
q	The Q matrix.
f	The F matrix.
years	The years matrix.

Definition at line 89 of file jade.neoscan.hpp.

            : _g     (g)
            , _q     (q)
            , _f     (f)
            , _y     (_init_y(years, q))
            , _f_j   (f.get_height(), 1)
        {
            verification_type::validate_gqf_sizes(g, q, f);
        }

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Member Function Documentation

execute()

template<typename TValue >

template<typename TOutputAction >

void jade::basic_neoscan< TValue >::execute ( const TOutputAction &  output_action ) const

inline

Executes the algorithm using the specified action for the output of each column.

Parameters

output_action

The action to perform for the output; this function or lambda must take one argument of type, output.

Definition at line 112 of file jade.neoscan.hpp.

        {
            const auto J = _g.get_width();
 
            for (size_t j = 0; j < J; j++)
            {
                value_type col_min = 0;
                value_type col_max = 0;
                _f.get_min_max_column(j, col_min, col_max);
 
                const auto range_low  = -col_max;
                const auto range_high = value_type(1.0) - col_min;
 
                output out;
                out.delta      = value_type(0.0);
                out.global_lle = _compute_lle_j(j, out.delta);
                out.local_lle  = out.global_lle;
 
                static const auto tol = value_type(0.000001);
                static const auto phi = value_type(0.5 * (sqrt(5.0) + 1.0));
 
                const auto dr_phi = (range_high - range_low) / phi;
 
                auto a = range_low;
                auto b = range_high;
                auto c = range_high - dr_phi;
                auto d = range_low  + dr_phi;
 
                while (std::abs(c - d) > tol)
                {
                    if (_compute_lle_j(j, c) > _compute_lle_j(j, d))
                        b = d;
                    else
                        a = c;
 
                    c = b - (b - a) / phi;
                    d = a + (b - a) / phi;
                }
 
                const auto gss_delta = value_type(0.5) * (a + b);
                const auto gss_lle   = _compute_lle_j(j, gss_delta);
 
                if (gss_lle > out.local_lle)
                {
                    out.delta     = gss_delta;
                    out.local_lle = gss_lle;
                }
 
                output_action(out);
            }
        }

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run()

template<typename TValue >

static void jade::basic_neoscan< TValue >::run ( args &  a )

inlinestatic

Runs the program based on command-line arguments.

Parameters

a	The command-line arguments.

Definition at line 168 of file jade.neoscan.hpp.

        {
            const std::unique_ptr<genotype_matrix_type> g_ptr (
                genotype_matrix_factory_type::create(a.pop<std::string>()));
 
            const matrix_type q (a.pop<std::string>());
            const matrix_type f (a.pop<std::string>());
            const matrix_type y (a.pop<std::string>());
            a.validate_empty();
 
            std::cout << "d\tglobal_lle\tlocal_lle\tlle_ratio\n";
 
            const basic_neoscan neoscan (*g_ptr, q, f, y);
 
            neoscan.execute([](const output & out)
            {
                std::cout << out.to_string() << std::endl;
            });
        }

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The documentation for this class was generated from the following file:

• jade.neoscan.hpp