structure.hpp File Reference

#include "genesis/population/functions/functions.hpp"
#include "genesis/population/variant.hpp"
#include "genesis/utils/containers/matrix.hpp"
#include "genesis/utils/containers/transform_iterator.hpp"
#include <algorithm>
#include <cassert>
#include <cmath>
#include <stdexcept>
#include <string>
#include <utility>
#include <vector>

Go to the source code of this file.

Namespaces
	genesis
	Container namespace for all symbols of genesis in order to keep them separate when used as a library.
	genesis::population

Functions
template<class ForwardIterator1 , class ForwardIterator2 >
double	f_st_pool_karlsson (ForwardIterator1 p1_begin, ForwardIterator1 p1_end, ForwardIterator2 p2_begin, ForwardIterator2 p2_end)
	Compute the F_ST statistic for pool-sequenced data of Karlsson et al as used in PoPoolation2, for two ranges of BaseCountss. More...
std::pair< double, double >	f_st_pool_karlsson_nkdk (std::pair< SortedBaseCounts, SortedBaseCounts > const &sample_counts)
	Compute the numerator N_k and denominator D_k needed for the asymptotically unbiased F_ST estimator of Karlsson et al (2007). More...
template<class ForwardIterator1 , class ForwardIterator2 >
double	f_st_pool_kofler (size_t p1_poolsize, size_t p2_poolsize, ForwardIterator1 p1_begin, ForwardIterator1 p1_end, ForwardIterator2 p2_begin, ForwardIterator2 p2_end)
	Compute the F_ST statistic for pool-sequenced data of Kofler et al as used in PoPoolation2, for two ranges of BaseCountss. More...
std::tuple< double, double, double >	f_st_pool_kofler_pi_snp (BaseCounts const &p1, BaseCounts const &p2)
	Compute the SNP-based Theta Pi values used in f_st_pool_kofler(). More...
template<class ForwardIterator1 , class ForwardIterator2 >
std::pair< double, double >	f_st_pool_unbiased (size_t p1_poolsize, size_t p2_poolsize, ForwardIterator1 p1_begin, ForwardIterator1 p1_end, ForwardIterator2 p2_begin, ForwardIterator2 p2_end)
	Compute our unbiased F_ST statistic for pool-sequenced data for two ranges of BaseCountss. More...
std::tuple< double, double, double >	f_st_pool_unbiased_pi_snp (size_t p1_poolsize, size_t p2_poolsize, BaseCounts const &p1, BaseCounts const &p2)
	Compute the SNP-based Theta Pi values used in f_st_pool_unbiased(). More...