FstPoolCalculatorKarlsson Class Reference

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

Inherits BaseFstPoolCalculator.

Detailed Description

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

The approach is called the "asymptotically unbiased" estimator in PoPoolation2 [1], and follows Karlsson et al [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] Efficient mapping of mendelian traits in dogs through genome-wide association.
Karlsson EK, Baranowska I, Wade CM, Salmon Hillbertz NHC, Zody MC, Anderson N, Biagi TM, Patterson N, Pielberg GR, Kulbokas EJ, Comstock KE, Keller ET, Mesirov JP, Von Euler H, Kämpe O, Hedhammar Å, Lander ES, Andersson G, Andersson L, Lindblad-Toh K.
Nature Genetics, 2007, 39(11), 1321–1328. https://doi.org/10.1038/ng.2007.10

Definition at line 73 of file fst_pool_karlsson.hpp.

Public Member Functions
	FstPoolCalculatorKarlsson ()=default
	FstPoolCalculatorKarlsson (FstPoolCalculatorKarlsson &&)=default
	FstPoolCalculatorKarlsson (FstPoolCalculatorKarlsson const &)=default
	FstPoolCalculatorKarlsson (size_t p1_poolsize, size_t p2_poolsize)
	Constructor that takes dummy pool sizes that are not used. Offered to have the same interface as the other FstPoolCalculator classes. More...
virtual	~FstPoolCalculatorKarlsson () override=default
FstPoolCalculatorKarlsson &	operator= (FstPoolCalculatorKarlsson &&)=default
FstPoolCalculatorKarlsson &	operator= (FstPoolCalculatorKarlsson 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::pair< double, double >	f_st_pool_karlsson_nkdk (std::pair< SortedSampleCounts, SortedSampleCounts > 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...

Additional Inherited Members

Constructor & Destructor Documentation

FstPoolCalculatorKarlsson() [1/4]

FstPoolCalculatorKarlsson ( )

default

FstPoolCalculatorKarlsson() [2/4]

FstPoolCalculatorKarlsson ( size_t  p1_poolsize, size_t  p2_poolsize  )

inline

Constructor that takes dummy pool sizes that are not used. Offered to have the same interface as the other FstPoolCalculator classes.

Definition at line 87 of file fst_pool_karlsson.hpp.

~FstPoolCalculatorKarlsson()

virtual ~FstPoolCalculatorKarlsson ( )

overridevirtualdefault

FstPoolCalculatorKarlsson() [3/4]

FstPoolCalculatorKarlsson ( FstPoolCalculatorKarlsson const &  )

default

FstPoolCalculatorKarlsson() [4/4]

FstPoolCalculatorKarlsson ( FstPoolCalculatorKarlsson &&  )

default

Member Function Documentation

f_st_pool_karlsson_nkdk()

static std::pair<double, double> f_st_pool_karlsson_nkdk ( std::pair< SortedSampleCounts, SortedSampleCounts > const &  sample_counts )

inlinestatic

Compute the numerator N_k and denominator D_k needed for the asymptotically unbiased F_ST estimator of Karlsson et al (2007).

See f_st_pool_karlsson() for details. The function expects sorted base counts for the two samples of which we want to compute F_ST, which are produced by sorted_average_sample_counts().

Definition at line 140 of file fst_pool_karlsson.hpp.

operator=() [1/2]

FstPoolCalculatorKarlsson& operator= ( FstPoolCalculatorKarlsson &&  )

default

operator=() [2/2]

FstPoolCalculatorKarlsson& operator= ( FstPoolCalculatorKarlsson const &  )

default

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

• fst_pool_karlsson.hpp