permtest.h File Reference

#include <memory>
#include <mutex>
#include "app.h"
#include "progressbar.h"
#include "thread.h"
#include "thread_queue.h"
#include "types.h"
#include "math/math.h"
#include "math/stats/glm.h"
#include "math/stats/shuffle.h"
#include "math/stats/typedefs.h"
#include "stats/enhance.h"

Go to the source code of this file.

Classes
class	MR::Stats::PermTest::PreProcessor
class	MR::Stats::PermTest::Processor

Namespaces
namespace	MR
namespace	MR::Stats
namespace	MR::Stats::PermTest

Macros
#define	DEFAULT_NUMBER_PERMUTATIONS   5000
#define	DEFAULT_NUMBER_PERMUTATIONS_NONSTATIONARITY   5000

Typedefs
using	MR::Stats::PermTest::value_type = Math::Stats::value_type
using	MR::Stats::PermTest::vector_type = Math::Stats::vector_type
using	MR::Stats::PermTest::matrix_type = Math::Stats::matrix_type
using	MR::Stats::PermTest::count_matrix_type = Eigen::Array< uint32_t, Eigen::Dynamic, Eigen::Dynamic >

Functions
void	MR::Stats::PermTest::precompute_empirical_stat (const std::shared_ptr< Math::Stats::GLM::TestBase > stats_calculator, const std::shared_ptr< EnhancerBase > enhancer, const default_type skew, matrix_type &empirical_statistic)
void	MR::Stats::PermTest::precompute_default_permutation (const std::shared_ptr< Math::Stats::GLM::TestBase > stats_calculator, const std::shared_ptr< EnhancerBase > enhancer, const matrix_type &empirical_enhanced_statistic, matrix_type &output_statistics, matrix_type &output_zstats, matrix_type &output_enhanced)
void	MR::Stats::PermTest::run_permutations (const std::shared_ptr< Math::Stats::GLM::TestBase > stats_calculator, const std::shared_ptr< EnhancerBase > enhancer, const matrix_type &empirical_enhanced_statistic, const matrix_type &default_enhanced_statistics, const bool fwe_strong, matrix_type &perm_dist, count_matrix_type &perm_dist_contributions, matrix_type &uncorrected_pvalues)

Macro Definition Documentation

DEFAULT_NUMBER_PERMUTATIONS

#define DEFAULT_NUMBER_PERMUTATIONS   5000

Definition at line 36 of file permtest.h.

DEFAULT_NUMBER_PERMUTATIONS_NONSTATIONARITY

#define DEFAULT_NUMBER_PERMUTATIONS_NONSTATIONARITY   5000

Definition at line 37 of file permtest.h.