Analyzes linkage disequilibrium per pair of polymorphic sites. More...

#include <LinkageDisequilibrium.hpp>

Inheritance diagram for LinkageDisequilibrium:

Public Member Functions
	LinkageDisequilibrium ()
	Default constructor.

virtual	~LinkageDisequilibrium ()
	Destructor.

void	load (CharMatrix &data, double minimumExploitableData=1., unsigned int ignoreFrequency=0, std::string characterMapping=dnaMapping)
	Analyzes polymorphic sites of an alignment. More...

unsigned int	numberOfPairs () const
	Number of pairs contained in the instance.

int	d (unsigned int pair_index)
	Alignment distance between a given pair.

double	D (unsigned int pair_index)
	D statistic for a given pair.

double	Dp (unsigned int pair_index)
	D' statistic for a given pair.

double	r (unsigned int pair_index)
	r statistic for a given pair

double	r2 (unsigned int pair_index)
	r2 statistic for a given pair

unsigned int	site1 (unsigned int pair_index)
	position of the first site for a given pair

unsigned int	site2 (unsigned int pair_index)
	position of the second site for a given pair

double	correl () const
	correlation coefficient between r2 and distance

unsigned int	Rmin (CharMatrix &data) const
	Computes the minimal number of recombination events. 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.

Protected Member Functions
void	add (CharMatrix &data, unsigned int position1, unsigned int position2)

void	init ()

void	clear ()

void	reset ()
	Clears and re-initializes object.

double	min (double a, double b)

double	max (double a, double b)

void	check (unsigned int pos)

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

Static Protected Member Functions
static void	_correl (unsigned int n, const int x, const double y, double &r, double &a)

Protected Attributes
int *	_d

double *	_D

double *	_Dp

double *	_r

double *	_r2

unsigned int *	_site1

unsigned int *	_site2

unsigned int	_n

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

Analyzes linkage disequilibrium per pair of polymorphic sites.

The class considers an alignment and detects polymorphic sites using the BaseDiversity functionality (shared with other classes of the module). Only sites with exactly two alleles are considered. Statistics of pairwise linkage disequilibrium can be accessed by pair index (note that out-of-range errors are not checked). Population labels are ignored (but outgroups are excluded from the analysis).

Member Function Documentation

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

Analyzes polymorphic sites of an alignment.

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".
minimumExploitableData	site 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.
ignoreFrequency	removes sites that are polymorphic 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.

unsigned int Rmin ( CharMatrix & data ) const

Computes the minimal number of recombination events.

The computation is performed as described in Hudson, RR and NL Kaplan. 1985. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111: 147-164. The returned parameter is the minimal number of recombination events, given by the number of non-overlapping pairs of segregating sites violating the rule of the four gamete. Only sites with two alleles are considered. Note that homoplasy (multiple mutations) mimicks recombination. The result of this function is not stored in this instance, and re-computed at each call.

Parameters

data	the same CharMatrix instance as passed to the load method. The instance must not have been modified.

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

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

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation