NucleotideDiversity Class Reference

Performs analyzes of population genetics. More...

#include <NucleotideDiversity.hpp>

Inheritance diagram for NucleotideDiversity:

Public Member Functions
	NucleotideDiversity ()
	Builds an object. More...
virtual	~NucleotideDiversity ()
	Destroys an object. More...
virtual void	load (CharMatrix &data, bool allowMultipleMutations=false, double minimumExploitableData=1., unsigned int ignoreFrequency=0, std::string characterMapping=dnaMapping, bool useZeroAsAncestral=false)
	Identifies polymorphic sites and computes basis statistics. More...
unsigned int	S () const
	Number of polymorphic sites.
unsigned int	So () const
	Number of polymorphic orientable sites.
unsigned int	eta () const
	Minimum number of mutations.
double	nseff () const
	Average of per-site number of sequences effectively used.
unsigned int	lseff () const
	Number of sites effectively used.
double	nseffo () const
	Average of number of sequences effectively used at orientable sites.
unsigned int	lseffo () const
	Number of orientable sites.
unsigned int	npop () const
	Number of detected populations.
unsigned int	popLabel (unsigned int popIndex) const
	Label of the population with given index (unsecure)
double	Pi ()
	Nucleotide diversity.
double	thetaW ()
	Watterson estimator of theta.
double	average_Pi ()
	Average of Pi over populations.
double	pop_Pi (unsigned int popIndex)
	Pi of a given population (unsecure)
double	D ()
	Tajima's D.
double	thetaH ()
	Fay and Wu estimator of theta.
double	thetaL ()
	Zeng et al. estimator of theta.
double	H ()
	Fay and Wu's H.
double	Z ()
	Standardized H.
double	E ()
	Zeng et al.'s E.
unsigned int	FixedDifferences ()
	Number of sites with at least one fixed difference.
unsigned int	CommonAlleles ()
	Number of sites with at least one allele shared among at least two populations.
unsigned int	SharedAlleles ()
	Number of sites with at least one non-fixed allele shared among at least two populations.
unsigned int	SpecificAlleles ()
	Number of sites with at least one allele specific to one population.
unsigned int	SpecificDerivedAlleles ()
	Number of sites with at least one derived allele specific to one population.
unsigned int	Polymorphisms (unsigned int pop)
	Number of polymorphisms in a given population (unsecure)
unsigned int	SpecificAlleles (unsigned int pop)
	Number of specific alleles for a given population (unsecure)
unsigned int	SpecificDerivedAlleles (unsigned int pop)
	Number of specific derived allele for a given population (unsecure)
unsigned int	FixedDifferences (unsigned int pop1, unsigned int pop2)
	Number of fixed differences between a given pair of populations (unsecure; pop2 must be larger than pop1)
unsigned int	CommonAlleles (unsigned int pop1, unsigned int pop2)
	Number of common alleles between a given pair of populations (unsecure; pop2 must be larger than pop1)
unsigned int	SharedAlleles (unsigned int pop1, unsigned int pop2)
	Number of shared non-fixed alleles between a given pair of populations (unsecure; pop2 must be larger than pop1)
unsigned int	triConfiguration (unsigned int index)
	Number falling into one of the possible site configurations. More...
std::vector< unsigned int >	polymorphic_positions () const
	Builds and returns the vector of positions of all polymorphic sites.
std::vector< unsigned int >	singleton_positions () const
	Builds and returns the vector of positions of all singleton sites. More...
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
	NucleotideDiversity (const NucleotideDiversity &source)
	This class cannot be copied. More...
NucleotideDiversity &	operator= (const NucleotideDiversity &source)
	This class cannot be copied. More...
void	init ()
void	clear ()
void	diversity ()
void	outgroupDiversity ()
void	differentiation ()
void	triConfigurations ()
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	b_analysisSites
bool	b_diversity
double	v_Pi
double	v_thetaW
double	v_average_Pi
double *	v_pop_Pi
double	v_D
bool	b_outgroupDiversity
double	v_thetaH
double	v_thetaL
double	v_H
double	v_Z
double	v_E
bool	b_differentiation
unsigned int *	v_pairwiseFixedDifferences
unsigned int *	v_pairwiseCommonAlleles
unsigned int *	v_pairwiseSharedAlleles
unsigned int *	v_popPolymorphic
unsigned int *	v_popSpecific
unsigned int *	v_popSpecificDerived
unsigned int	v_countFixedDifferences
unsigned int	v_countCommonAlleles
unsigned int	v_countSharedAlleles
unsigned int	v_countSpecificAlleles
unsigned int	v_countSpecificDerivedAlleles
bool	b_triConfigurations
unsigned int *	v_triConfigurations
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

Performs analyzes of population genetics.

This class computes several summary statistics based on nucleotide analysis. Note that it is possible to use the same object to analyze different data set. Calling the load() method erases all data preivously computed (if any). Calling the load() method is absolutely required to compute any statistics. Some statistics are not computed by default, but are if the corresponding accessor is used (only load() is required).

Note that "unsecure" accessors don't perform out-of-bound checks.

S is the number of varying sites (only in sites that were not rejected).

eta is the minimum number of mutations, that is the sum of the number of alleles minus 1 for each varying site. eta = S if all sites have no variant or 2 alleles. eta is computed independently of the option multiple and IS NOT computed over lseff sites.

Pi is the average number of pairwise differences between sequences (expressed here per site) or (as computed here) the mean per site (unbiased) heterozygosity. Pi is zero if no polymorphic sites.

D is the Tajima's test of neutrality Ref. Tajima F.: Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 1989, 123:585-595. It is arbitrary set to 0 if no polymorphic sites.

tW: thetaW: estimator of theta based on polymorphic sites (ref. e.g. Watterson 1975 Theor. Pop. Biol.). Both D and thetaW are computed assuming that rounded nseff samples have been sampled. The variance of D is computed using rounded nseff instead of ns.

H is the Fay and Wu's test of neutrality. Z is the standardized version and E a similar test. Ref. Fay J. C., Wu C.-I.: Hitchhiking under positive Darwinian selection. Genetics 2000, 155:1405-1413. and Zeng K., Fu Y. X., Shi S., Wu C.-I.: Statistical tests for detecting positive selection by utilizing high-frequency variants. Genetics 2006, 174:1431-9. Both are arbitrary set to 0 if no polymorphic or orientable sites.

tH and tL: theta H: estimators of theta based on derived polymorphic sites (ref in Fay and Wu and Zeng al.). The variance of H/Z are computed assuming that rounded nseff samples have been sampled.

Constructor & Destructor Documentation

NucleotideDiversity

(

)

Builds an object.

~NucleotideDiversity ( )

virtual

Destroys an object.

NucleotideDiversity ( const NucleotideDiversity &  source )

inlineprotected

This class cannot be copied.

Member Function Documentation

void load ( CharMatrix &  data, bool  allowMultipleMutations = false, double  minimumExploitableData = 1., unsigned int  ignoreFrequency = 0, std::string  characterMapping = dnaMapping, bool  useZeroAsAncestral = false  )

virtual

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).
minimumExploitableData	sites where the non-missing data (as defined by characterMapping) are at a frequency larger than this value will be removed from the analysis. Use 1. to take only 'complete' sites into account and 0. to use all sites. (The outgroup is not considered in this computation.)
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=0, 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.
useZeroAsAncestral	if true, all outgroups (if present) will be ignored and the character "0" will be considered as ancestral for all sites, whatever the character mapping.

NucleotideDiversity& operator= ( const NucleotideDiversity &  source )

inlineprotected

This class cannot be copied.

std::vector< unsigned int > singleton_positions

(

)

const

Builds and returns the vector of positions of all singleton sites.

A site singleton when it is polymorphic according to parameter of the diversity analysis, when it has exactly two alleles and one of them is at absolute frequency 1 (one copy) disregarding the outgroup.

unsigned int triConfiguration

(

unsigned int

index

)

Number falling into one of the possible site configurations.

The statistics are limited to three populations. Assuming an unrooted A/G polymorphism (A and G can be substitued), the site configurations are:

• 0: A&G A A specific 1
• 1: A&G A G specific 1 + fixed 2-3
• 2: A A&G A specific 2
• 3: A A&G G specific 2 + fixed 1-3
• 4: A A A&G specific 3
• 5: A G A&G specific 3 + fixed 1-2
• 6: A&G A&G A shared 1-2
• 7: A&G A A&G shared 1-3
• 8: A A&G A&G shared 2-3
• 9: A&G A&G A&G shared 1-2-3
• 10: A G G fixed 1
• 11: A G A fixed 2
• 12: A A G fixed 3

Parameters

index

must be an index from 0 to 12.

---

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

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