FstPoolCalculatorKofler Class Reference

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

Inherits BaseFstPoolCalculator.

Detailed Description

Compute the F_ST statistic for pool-sequenced data of Kofler et al as used in PoPoolation2, for two ranges of SampleCountss.

The approach is called the "classical" or "conventional" estimator in PoPoolation2 [1], and follows Hartl and Clark [2].

[1] PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq).
Kofler R, Pandey RV, Schlotterer C.
Bioinformatics, 2011, 27(24), 3435–3436. https://doi.org/10.1093/bioinformatics/btr589

[2] Principles of Population Genetics.
Hartl DL, Clark AG.
Sinauer, 2007.

Definition at line 70 of file fst_pool_kofler.hpp.

Public Member Functions
	FstPoolCalculatorKofler (FstPoolCalculatorKofler &&)=default
	FstPoolCalculatorKofler (FstPoolCalculatorKofler const &)=default
	FstPoolCalculatorKofler (size_t p1_poolsize, size_t p2_poolsize)
virtual	~FstPoolCalculatorKofler () override=default
FstPoolCalculatorKofler &	operator= (FstPoolCalculatorKofler &&)=default
FstPoolCalculatorKofler &	operator= (FstPoolCalculatorKofler 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 ()

Static Public Member Functions
static std::tuple< double, double, double >	f_st_pool_kofler_pi_snp (SampleCounts const &p1, SampleCounts const &p2)
	Compute the SNP-based Theta Pi values used above. More...

Additional Inherited Members

Constructor & Destructor Documentation

FstPoolCalculatorKofler() [1/3]

FstPoolCalculatorKofler ( size_t  p1_poolsize, size_t  p2_poolsize  )

inline

Definition at line 78 of file fst_pool_kofler.hpp.

~FstPoolCalculatorKofler()

virtual ~FstPoolCalculatorKofler ( )

overridevirtualdefault

FstPoolCalculatorKofler() [2/3]

FstPoolCalculatorKofler ( FstPoolCalculatorKofler const &  )

default

FstPoolCalculatorKofler() [3/3]

FstPoolCalculatorKofler ( FstPoolCalculatorKofler &&  )

default

Member Function Documentation

f_st_pool_kofler_pi_snp()

static std::tuple<double, double, double> f_st_pool_kofler_pi_snp ( SampleCounts const &  p1, SampleCounts const &  p2  )

inlinestatic

Compute the SNP-based Theta Pi values used above.

See there for details. The tuple returns Theta Pi for an individual position, which is simply the heterozygosity() at this position, for both samples p1 and p2, as well as their combined (average frequency) heterozygosity, in that order.

Definition at line 174 of file fst_pool_kofler.hpp.

operator=() [1/2]

FstPoolCalculatorKofler& operator= ( FstPoolCalculatorKofler &&  )

default

operator=() [2/2]

FstPoolCalculatorKofler& operator= ( FstPoolCalculatorKofler const &  )

default

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

• fst_pool_kofler.hpp