#include <genesis/population/function/fst_pool_unbiased.hpp>

Detailed Description

Compute our unbiased F_ST statistic for pool-sequenced data for two ranges of SampleCountss.

This is our novel approach for estimating F_ST, using pool-sequencing corrected estimates of Pi within, Pi between, and Pi total, to compute F_ST following the definitions of Nei [1] and Hudson [2], respectively. These are returned here as a pair in that order. See https://github.com/lczech/pool-seq-pop-gen-stats for details.

[1] Analysis of Gene Diversity in Subdivided Populations.
Nei M.
Proceedings of the National Academy of Sciences, 1973, 70(12), 3321–3323. https://doi.org/10.1073/PNAS.70.12.3321

[2] Estimation of levels of gene flow from DNA sequence data.
Hudson RR, Slatkin M, Maddison WP.
Genetics, 1992, 132(2), 583–589. https://doi.org/10.1093/GENETICS/132.2.583

Definition at line 82 of file fst_pool_unbiased.hpp.

Public Member Functions
	FstPoolCalculatorUnbiased (FstPoolCalculatorUnbiased &&)=default

	FstPoolCalculatorUnbiased (FstPoolCalculatorUnbiased const &)=default

	FstPoolCalculatorUnbiased (size_t smp1_poolsize, size_t smp2_poolsize, WindowAveragePolicy window_average_policy, Estimator est=Estimator::kNei)

virtual	~FstPoolCalculatorUnbiased () override=default

double	get_pi_between () const

template<class D >
double	get_pi_between (BaseWindow< D > const &window, std::shared_ptr< GenomeLocusSet > provided_loci, VariantFilterStats const &variant_filter_stats) const

double	get_pi_total () const

template<class D >
double	get_pi_total (BaseWindow< D > const &window, std::shared_ptr< GenomeLocusSet > provided_loci, VariantFilterStats const &variant_filter_stats) const

double	get_pi_total (double pi_within, double pi_between) const

PiValues	get_pi_values () const

template<class D >
PiValues	get_pi_values (BaseWindow< D > const &window, std::shared_ptr< GenomeLocusSet > provided_loci, VariantFilterStats const &variant_filter_stats) const

double	get_pi_within () const

template<class D >
double	get_pi_within (BaseWindow< D > const &window, std::shared_ptr< GenomeLocusSet > provided_loci, VariantFilterStats const &variant_filter_stats) const

template<class D >
double	get_result (BaseWindow< D > const &window, std::shared_ptr< GenomeLocusSet > provided_loci, VariantFilterStats const &variant_filter_stats) const

std::pair< double, double >	get_result_pair () const
	Get both variants of FST, following Nei, and following Hudson, as a pair. More...

template<class D >
std::pair< double, double >	get_result_pair (BaseWindow< D > const &window, std::shared_ptr< GenomeLocusSet > provided_loci, VariantFilterStats const &variant_filter_stats) const
	Get both variants of FST, following Nei, and following Hudson, as a pair. More...

WindowAveragePolicy	get_window_average_policy () const

FstPoolCalculatorUnbiased &	operator= (FstPoolCalculatorUnbiased &&)=default

FstPoolCalculatorUnbiased &	operator= (FstPoolCalculatorUnbiased const &)=default

Public Member Functions inherited from BaseFstPoolCalculator
	BaseFstPoolCalculator ()=default

	BaseFstPoolCalculator (BaseFstPoolCalculator &&)=default

	BaseFstPoolCalculator (BaseFstPoolCalculator const &)=default

virtual	~BaseFstPoolCalculator ()=default

SampleCountsFilterStats	get_filter_stats () const
	Get the sum of filter statistics of all sample pairs processed here. More...

double	get_result () const

BaseFstPoolCalculator &	operator= (BaseFstPoolCalculator &&)=default

BaseFstPoolCalculator &	operator= (BaseFstPoolCalculator const &)=default

void	process (SampleCounts const &p1, SampleCounts const &p2)

void	reset ()

Public Types
enum	Estimator { kNei, kHudson }

Classes
struct	PiValues

Additional Inherited Members

Constructor & Destructor Documentation

◆ FstPoolCalculatorUnbiased() [1/3]

FstPoolCalculatorUnbiased	(	size_t	smp1_poolsize,
		size_t	smp2_poolsize,
		WindowAveragePolicy	window_average_policy,
		Estimator	est = `Estimator::kNei`
	)

inline

Definition at line 107 of file fst_pool_unbiased.hpp.

◆ ~FstPoolCalculatorUnbiased()

virtual ~FstPoolCalculatorUnbiased ( )

overridevirtualdefault

◆ FstPoolCalculatorUnbiased() [2/3]

FstPoolCalculatorUnbiased ( FstPoolCalculatorUnbiased const & )

default

◆ FstPoolCalculatorUnbiased() [3/3]

FstPoolCalculatorUnbiased ( FstPoolCalculatorUnbiased && )

default

Member Function Documentation

◆ get_pi_between() [1/2]

double get_pi_between ( ) const

inline

Definition at line 395 of file fst_pool_unbiased.hpp.

◆ get_pi_between() [2/2]

double get_pi_between	(	BaseWindow< D > const &	window,
		std::shared_ptr< GenomeLocusSet >	provided_loci,
		VariantFilterStats const &	variant_filter_stats
	)		const

inline

Definition at line 325 of file fst_pool_unbiased.hpp.

◆ get_pi_total() [1/3]

double get_pi_total ( ) const

inline

Definition at line 400 of file fst_pool_unbiased.hpp.

◆ get_pi_total() [2/3]

double get_pi_total	(	BaseWindow< D > const &	window,
		std::shared_ptr< GenomeLocusSet >	provided_loci,
		VariantFilterStats const &	variant_filter_stats
	)		const

inline

Definition at line 341 of file fst_pool_unbiased.hpp.

◆ get_pi_total() [3/3]

double get_pi_total	(	double	pi_within,
		double	pi_between
	)		const

inline

Definition at line 335 of file fst_pool_unbiased.hpp.

◆ get_pi_values() [1/2]

PiValues get_pi_values ( ) const

inline

Definition at line 407 of file fst_pool_unbiased.hpp.

◆ get_pi_values() [2/2]

PiValues get_pi_values	(	BaseWindow< D > const &	window,
		std::shared_ptr< GenomeLocusSet >	provided_loci,
		VariantFilterStats const &	variant_filter_stats
	)		const

inline

Definition at line 352 of file fst_pool_unbiased.hpp.

◆ get_pi_within() [1/2]

double get_pi_within ( ) const

inline

Definition at line 388 of file fst_pool_unbiased.hpp.

◆ get_pi_within() [2/2]

double get_pi_within	(	BaseWindow< D > const &	window,
		std::shared_ptr< GenomeLocusSet >	provided_loci,
		VariantFilterStats const &	variant_filter_stats
	)		const

inline

Definition at line 310 of file fst_pool_unbiased.hpp.

◆ get_result()

double get_result	(	BaseWindow< D > const &	window,
		std::shared_ptr< GenomeLocusSet >	provided_loci,
		VariantFilterStats const &	variant_filter_stats
	)		const

inline

Definition at line 270 of file fst_pool_unbiased.hpp.

◆ get_result_pair() [1/2]

std::pair<double, double> get_result_pair ( ) const

inline

Get both variants of FST, following Nei, and following Hudson, as a pair.

Definition at line 376 of file fst_pool_unbiased.hpp.

◆ get_result_pair() [2/2]

std::pair<double, double> get_result_pair	(	BaseWindow< D > const &	window,
		std::shared_ptr< GenomeLocusSet >	provided_loci,
		VariantFilterStats const &	variant_filter_stats
	)		const

inline

Get both variants of FST, following Nei, and following Hudson, as a pair.

Definition at line 293 of file fst_pool_unbiased.hpp.

◆ get_window_average_policy()

WindowAveragePolicy get_window_average_policy ( ) const

inline

Definition at line 364 of file fst_pool_unbiased.hpp.

◆ operator=() [1/2]

FstPoolCalculatorUnbiased& operator= ( FstPoolCalculatorUnbiased && )

default

◆ operator=() [2/2]

FstPoolCalculatorUnbiased& operator= ( FstPoolCalculatorUnbiased const & )

default

Member Enumeration Documentation

◆ Estimator

enum Estimator

strong

Enumerator
kNei
kHudson

Definition at line 90 of file fst_pool_unbiased.hpp.

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

fst_pool_unbiased.hpp

Detailed Description

Public Member Functions

Public Types

Classes

Additional Inherited Members

Constructor & Destructor Documentation

◆ FstPoolCalculatorUnbiased() [1/3]

◆ ~FstPoolCalculatorUnbiased()

◆ FstPoolCalculatorUnbiased() [2/3]

◆ FstPoolCalculatorUnbiased() [3/3]

Member Function Documentation

◆ get_pi_between() [1/2]

◆ get_pi_between() [2/2]

◆ get_pi_total() [1/3]

◆ get_pi_total() [2/3]

◆ get_pi_total() [3/3]

◆ get_pi_values() [1/2]

◆ get_pi_values() [2/2]

◆ get_pi_within() [1/2]

◆ get_pi_within() [2/2]

◆ get_result()

◆ get_result_pair() [1/2]

◆ get_result_pair() [2/2]

◆ get_window_average_policy()

◆ operator=() [1/2]

◆ operator=() [2/2]

Member Enumeration Documentation

◆ Estimator