models Class Reference

#include <models.h>

Collaboration diagram for models:

Public Member Functions
float_t	loglikelihood (const Locus &, const Allele &)
	Gets the log likelihood of the observations at Locus, given Allele. More...
float_t	goodness_of_fit (Locus &, const Allele &, std::vector< float_t > &, const float_t &)
	Gets the log likelihood of the observations at Locus, given Allele.
void	init_gof (const count_t *, const Allele &)
	breif Initilizes the ? for goodness of fit calculations.
float_t	get_gof (const count_t *, const Allele &)
	Returns the likelihood of a ?? goodness of fit... blah blah blah.
float_t	genotypelikelihood (const quartet_t &, const Allele &)
	Clalculates genotypic likelihoods. Not implement, may be depricated. More...
float_t	lnL (const float_t &logMM, const float_t &logMm, const float &logmm, const count_t *count)
	Clalculates goodness of fit likelihoods.
models &	operator= (const models &rhs)

Private Attributes
lnmultinomial	lnMM_
lnmultinomial	lnMm_
lnmultinomial	lnmm_
	The three multinomials we will use for probability calculations.
lnmultinomial	lnMMP_
lnmultinomial	lnMmP_
lnmultinomial	lnmmP_
float_t	E0_
float_t	E1_
float_t	E2_
	Values used in calculations;.

Detailed Description

this class perfoms some likelihood calculations. It keeps some look-up tables that will grow as calculations are performed, and may become to large over time. TODO: implement automatic look-up table purging.

Currently likelihood calculations are all performed by a set of 'models' that we give to the "multinomial" class via the multinomial::set method. These models should be able to look at the Allele structure, which contains information about the error rate at the locus and the identity of the major and minor allele, and return a set of four log probabilities of observing each particular nucleotide in a given call.

Member Function Documentation

float_t models::genotypelikelihood	(	const quartet_t &	quartet,
		const Allele &	population
	)

Clalculates genotypic likelihoods. Not implement, may be depricated.

DONT USE THIS!!! TODO FIX IT!.

float_t models::loglikelihood	(	const Locus &	site,
		const Allele &	p
	)

Gets the log likelihood of the observations at Locus, given Allele.

A function that calculates the logl likelihood of a set of observations.

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

• mapgd_0.4/math_functions/models.h
• mapgd_0.4/math_functions/models.cc