MicrosatelliteDiversity Class Reference

Analyzes microsatellite data. More...

#include <MicrosatelliteDiversity.hpp>

Public Member Functions
	MicrosatelliteDiversity ()
	Creates an object. More...
virtual	~MicrosatelliteDiversity ()
	Destroys an object. More...
void	load (const DataMatrix &dataMatrix, int missingData=999, bool noMissingData=false)
	Performs the analysis. More...
unsigned int	numberOfSites () const
	Number of sites (or markers)
double	He (unsigned int siteIndex) const
	Heterozygosity.
unsigned int	numberOfAlleles (unsigned int siteIndex) const
	Number of alleles.
double	sizeVariance (unsigned int siteIndex) const
	Variance of allele size.
double	thetaAssumingIAM (unsigned int siteIndex) const
	IAM-based estimator of theta.
double	thetaAssumingSMMfromHe (unsigned int siteIndex) const
	SMM-based estimator of theta, calculated from He.
double	thetaAssumingSMMfromSizeVariance (unsigned int siteIndex) const
	SMM-based estimator of theta, calculated from VarSize.

Protected Member Functions
void	init ()
void	clear ()

Protected Attributes
unsigned int	v_numberOfSites
double *	v_He
unsigned int *	v_numberOfAlleles
double *	v_sizeVariance
double *	v_thetaAssumingIAM
double *	v_thetaAssumingSMMfromHe
double *	v_thetaAssumingSMMfromSizeVariance

Detailed Description

Analyzes microsatellite data.

Use the load() method to analyze data. All sites will be analyzed and accessors allow to access the value of a given statistics for a given site. There is no out-of-bound checking implemented in accessors.

Constructor & Destructor Documentation

MicrosatelliteDiversity

(

)

Creates an object.

~MicrosatelliteDiversity ( )

virtual

Destroys an object.

Member Function Documentation

void load	(	const DataMatrix &	dataMatrix,
		int	missingData = 999,
		bool	noMissingData = false
	)

Performs the analysis.

Parameters

dataMatrix	the object to analyze.
missingData	the integer identifying missing data.
noMissingData	if true, no allele will be excluded (including the one identified by the argument missingData).

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

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