Computes Fst and Fit from haploid data. More...

#include <HFStatistics.hpp>

Public Member Functions
	HFStatistics ()
	Constructor. More...

virtual	~HFStatistics ()
	Destructor. More...

void	reserve (unsigned int numberOfIndividuals)
	Reserve sufficient memory for a given number of individuals. More...

void	loadIndividual (unsigned int genotype, unsigned int populationLabel)
	Loads the data for one individual. More...

unsigned int	populationLabel (unsigned int populationIndex)
	Label of a population. More...

unsigned int	alleleValue (unsigned int alleleIndex)
	Value of an allele. More...

unsigned int	allele (unsigned int individualIndex) const
	Allele of a given individual (no checking)

unsigned int	individualLabel (unsigned int individualIndex) const
	Population label of a given individual (no checking)

unsigned int	numberOfAlleles ()
	Number of alleles. More...

unsigned int	numberOfPopulations ()
	Number of populations. More...

unsigned int	numberOfGenotypes () const
	Number of loaded genotypes. More...

unsigned int	alleleFrequencyTotal (unsigned int alleleIndex)
	Absolute total allele frequency. More...

unsigned int	alleleFrequencyPerPopulation (unsigned int populationIndex, unsigned int alleleIndex)
	Absolute allele frequency in a population. More...

unsigned int	populationFrequency (unsigned int populationIndex)
	Sample size of a population. More...

double	theta ()
	Weir-Cockerham theta-statistic. More...

double	T1 ()
	Between-population component of variance. More...

double	T2 ()
	Total variance. More...

Protected Member Functions
void	d_init ()

void	d_clear ()

void	s_init ()

void	s_clear ()

void	s_compute ()

void	processPopulations ()

void	processAlleles ()

unsigned int	getPopulationIndex (unsigned int) const

unsigned int	getAlleleIndex (unsigned int) const

void	w_init ()

void	w_clear ()

void	w_compute ()

Protected Attributes
bool	d_flag

unsigned int	d_reserved

unsigned int	d_numberOfGenotypes

unsigned int *	d_genotypes

unsigned int *	d_populationLabels

bool	s_flag

unsigned int	s_numberOfAlleles

unsigned int *	s_alleleValueMapping

unsigned int	s_numberOfPopulations

unsigned int *	s_populationLabelMapping

unsigned int *	s_populationFrequencies

unsigned int *	s_alleleFrequenciesTotal

unsigned int **	s_alleleFrequenciesPerPopulation

bool	w_flag

double	w_T

double *	w_T1

double *	w_T2

double	w_nbar

double	w_nc

double *	w_pbar

double *	w_ssquare

double	w_sum_T1

double	w_sum_T2

Detailed Description

Computes Fst and Fit from haploid data.

The class requires loading data. Data are loaded by haploid (one genotype per individual). The analyses are cached: they are performed upon the first call to statistics accessors. The cache is emptied whenever a datum is loaded.

The computations are performed after Weir and Cockerham. The statistic theta is generalized for multiple alleles. To allow computation of multi-locus statistics, variance components are also available. The two components of the variance are T1 and T2 and theta is T1/T2 (from Weir 1996 "Genetic Data Analysis II", Sinauer associates, Sunderland MA).

Constructor & Destructor Documentation

HFStatistics ( )

Constructor.

~HFStatistics ( )

virtual

Destructor.

Member Function Documentation

unsigned int alleleFrequencyPerPopulation	(	unsigned int	populationIndex,
		unsigned int	alleleIndex
	)

Absolute allele frequency in a population.

unsigned int alleleFrequencyTotal ( unsigned int alleleIndex )

Absolute total allele frequency.

unsigned int alleleValue ( unsigned int alleleIndex )

Value of an allele.

The index corresponds to the local mapping of alleles regardless of the ranking of allele values. (No out of bound checking.)

void loadIndividual	(	unsigned int	genotype,
		unsigned int	populationLabel
	)

Loads the data for one individual.

Parameters

genotype	an integer giving the allele.
populationLabel	an integer indication belonging to a population.

Genotypes and population labels are not required to be consecutive (both are labels, not indices). They are internally mapped to indices (the mapping can be obtained by accessors populationLabel and allele).

All genotypes are considered to be valid (no missing data). If statistics were computed previous to call to this function, all data will be erased.

unsigned int numberOfAlleles ( )

Number of alleles.

unsigned int numberOfGenotypes ( ) const

Number of loaded genotypes.

unsigned int numberOfPopulations ( )

Number of populations.

unsigned int populationFrequency ( unsigned int populationIndex )

Sample size of a population.

unsigned int populationLabel ( unsigned int populationIndex )

Label of a population.

The index corresponds to the local mapping of populations regardless of the ranking of population labels. (No out of bound checking.)

void reserve ( unsigned int numberOfIndividuals )

Reserve sufficient memory for a given number of individuals.

This method makes the load function faster by allocating all required memory at once.

Parameters

numberOfIndividuals a strictly positive integer.

double T1 ( )

Between-population component of variance.

double T2 ( )

Total variance.

double theta ( )

Weir-Cockerham theta-statistic.

Note: equivalent to Fst.

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

/home/stephane/Documents/devel/egglib2/egglib-cpp/HFStatistics.hpp
/home/stephane/Documents/devel/egglib2/egglib-cpp/HFStatistics.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation