HaplotypeDiversity Class Reference

Computes diversity based on haplotype analysis. More...

#include <HaplotypeDiversity.hpp>

Inheritance diagram for HaplotypeDiversity:

Public Member Functions
	HaplotypeDiversity ()
	Constructor. More...
virtual	~HaplotypeDiversity ()
	Destructor. More...
void	load (CharMatrix &data, bool allowMultipleMutations=false, unsigned int ignoreFrequency=0, std::string characterMapping=dnaMapping)
	Identifies polymorphic sites and computes basis statistics. More...
unsigned int	K () const
	Number of distinct haplotypes.
double	He () const
	Haplotype diversity (unbiased)
unsigned int	haplotypeIndex (unsigned int) const
	Returns the allele number of a given sequence. More...
double	Kst () const
	Population differenciation, based on nucleotides (Hudson 1992a)
double	Fst () const
	Population differenciation, based on nucleotides (Hudson 1992b)
double	Gst () const
	Population differenciation, based on haplotypes (Nei version)
double	Hst () const
	Population differenciation, based on haplotypes (Hudson et al. version)
double	Snn () const
	Hudson's Snn (nearest neighbor statistics)
Public Member Functions inherited from BaseDiversity
	BaseDiversity ()
	Constructor. More...
virtual	~BaseDiversity ()
	Destructor. More...
virtual void	reserve (unsigned int numberOfSites)
	Reserve sufficient memory for a given number of polymorphic sites. More...
const SitePolymorphism *	get_site (unsigned int index) const
	Gets a site.
unsigned int	get_position (unsigned int index) const
	Gets a site position.
virtual void	reset ()
	Clears and re-initializes object.

Protected Member Functions
void	init ()
void	clear ()
unsigned int	diff (CharMatrix &data, unsigned int ind1, unsigned int ind2) const
Protected Member Functions inherited from BaseDiversity
void	importSites (CharMatrix &data, bool allowMultipleMutations, double minimumExploitableData, unsigned int ignoreFrequency, std::string characterMapping, bool useZeroAsAncestral, bool ignoreOutgroup)
void	analyzeSite (CharMatrix &data, unsigned int index, double maxMissingData, bool ignoreOutgroup)
unsigned int	getPopIndex (unsigned int label) const

Protected Attributes
bool	m_loaded
unsigned int	m_K
double	m_He
double	m_Kst
double	m_Fst
double	m_Gst
double	m_Hst
double	m_Snn
unsigned int *	m_haplotypeIndex
Protected Attributes inherited from BaseDiversity
SitePolymorphism **	v_sites
bool *	v_orientables
unsigned int *	v_sitePositions
unsigned int	v_reserved
unsigned int	v_ns
unsigned int	v_S
unsigned int	v_So
unsigned int	v_eta
double	v_nseff
unsigned int	v_lseff
double	v_nseffo
unsigned int	v_lseffo
unsigned int	v_npop
unsigned int *	v_popLabel
bool	p_allowMultipleMutations
double	p_minimumExploitableData
std::string	p_characterMapping
unsigned int	p_pos_sep_mapping
bool	p_useZeroAsAncestral
unsigned int	p_ignoreFrequency

Additional Inherited Members
Static Public Attributes inherited from BaseDiversity
static const std::string	dnaMapping = "ACGT MRWSYKBDHVN?-"
	Predefined mapping string for DNA data. More...
static const std::string	rnaMapping = "ACGU MRWSYKBDHVN?-"
	Predefined mapping string for RNA data. More...
static const std::string	aaMapping = "GALMFWKQESPVICYHRNDT X-"
	Predefined mapping string for amino acid data. More...

Detailed Description

Computes diversity based on haplotype analysis.

This class relies on detection of polymorphic sites, as does NucleotideDiversity, with the exception that sites with missing data cannot be processed (minimumExploitableData is enforced to 1.).

Like NucleotideDiversity, the same object can be used to analyze different data sets. Only the call to load() is required before accessing the data.

Hst, Gst and Kst are between population differenciation indices. They are respectively defined in equations 2, 5-6 and 9 of Hudson et al. 1992a (Molecular Biology and Evolution 9:138-151). Also, Fst is defined in equation 3 of Hudson et al. 1992b (Genetics 132:583-589). Finally, Snn is from Hudson 2000 Genetics. It is computed as the average of Xi for all sequences. Where Xi is the ratio of nearest neighbours from the same group to the number of nearest neighbours. Nearest neigbours are all the sequences with the lowest number of differences to the focal sequence. NOTE: Gst/Hst are quite similar, but Fst and Kst are more different. Snn is a different statistic. Gst and Hst are two ways to estimate the between-population fraction of haplotypic diversity.

Constructor & Destructor Documentation

HaplotypeDiversity

(

)

Constructor.

~HaplotypeDiversity ( )

virtual

Destructor.

Member Function Documentation

unsigned int haplotypeIndex

(

unsigned int

index

)

const

Returns the allele number of a given sequence.

The passed index must be given ignoring any outgroup sequence.

void load	(	CharMatrix &	data,
		bool	allowMultipleMutations = false,
		unsigned int	ignoreFrequency = 0,
		std::string	characterMapping = dnaMapping
	)

Identifies polymorphic sites and computes basis statistics.

Parameters

data	an alignment object (subclass of CharMatrix). The presence of outgroup or of different populations will be detected based on the populationLabel members of the passed object. The populationLabel 999 will be interpreted as outgroups. If several outgroups are passed, sites were the outgroups are not consistent will be treated as "non- orientable".
allowMultipleMutations	if true, sites with more than two alleles will not be ignored. The sum of the frequencies of all alleles not matching the outgroup will treated as the derived allele frequency (for orientable sites).
ignoreFrequency	removes sites that are polymorph because of an allele at absolute frequency smaller than or equal to this value. If ignoreFrequency=1, no sites are removed, if ignoreFrequency=1, singleton sites are ignored. Such sites are completely removed from the analysis (not counted in lseff). Note that if more than one mutation is allowed, the site is removed only if all the alleles but one are smaller than or equal to this value. For example, an alignment column AAAAAAGAAT is ignored with an ignoreFrequency of 1, but AAAAAAGGAT is conserved (including the third allele T which is a singleton).
characterMapping	a string giving the list of characters that should be considered as valid data. If a space is present in the string, the characters left of the space will be treated as valid data and the characters right of the space will be treated as missing data, that is tolerated but ignored. All characters not in the string will cause an EggInvalidCharacterError to be raised.

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

• /home/stephane/Documents/devel/egglib2/egglib-cpp/HaplotypeDiversity.hpp
• /home/stephane/Documents/devel/egglib2/egglib-cpp/HaplotypeDiversity.cpp