Sequence::PolySIM Class Reference
[Analysis of molecular population genetic data]

Analysis of coalescent simulation data. More...

#include <Sequence/PolySIM.hpp>

Inheritance diagram for Sequence::PolySIM:

Public Member Functions
	PolySIM (const Sequence::SimData *data)
double	ThetaPi (void)
double	ThetaW (void)
double	ThetaH (void)
double	ThetaL (void)
unsigned	NumMutations (void)
unsigned	NumSingletons (void)
unsigned	NumExternalMutations (void)
double	TajimasD (void)
double	Hprime (bool likeThorntonAndolfatto=false)
double	Dnominator (void)
double	FuLiD (void)
double	FuLiF (void)
double	FuLiDStar (void)
double	FuLiFStar (void)
double	WallsB (void)
unsigned	WallsBprime (void)
double	WallsQ (void)
int	HudsonsHaplotypeTest (int subsize, int subss)
unsigned	Minrec (void)
double	VarPi (void)
double	StochasticVarPi (void)
double	SamplingVarPi (void)
double	VarThetaW (void)
unsigned	NumPoly (void)
double	DandVH (void)
unsigned	DandVK (void)
double	HudsonsC (void)
std::vector< std::vector < double > >	Disequilibrium (const unsigned &mincount=1, const double &max_marker_distance=std::numeric_limits< double >::max())
Protected Member Functions
void	WallStats (void)
void	DepaulisVeuilleStatistics (void)
double	a_sub_n (void)
double	a_sub_n_plus1 (void)
double	b_sub_n (void)
double	b_sub_n_plus1 (void)
double	c_sub_n (void)
double	d_sub_n (void)
Protected Attributes
std::auto_ptr< _PolySNPImpl >	rep

Detailed Description

Analysis of coalescent simulation data.

This class inherits from Sequence::PolySNP. It is a collection of analysis routines for coalescent simulation data, and is constructed from a const Sequence::SimData *. The main difference is that outgroup information is not required, as the 0,1 coding of a SimData object (usually) reflects ancestral and derived.

Examples:: bottleneck.cc, and msstats.cc.

Definition at line 44 of file PolySIM.hpp.

Constructor & Destructor Documentation

Sequence::PolySIM::PolySIM ( const Sequence::SimData * data ) [explicit]

Parameters:

data

a valid object of type Sequence::SimData

Definition at line 41 of file PolySIM.cc.

Member Function Documentation

double Sequence::PolySNP::a_sub_n ( void ) [protected, inherited]

$a_n=\sum_{i=1}^{i=n-1}\frac{1}{i}.\$

This is the denominator of Watterson's Theta (see PolySNP::ThetaW)

Warning:: statistic undefined if there are untyped SNPs

Definition at line 1149 of file PolySNP.cc.

double Sequence::PolySNP::a_sub_n_plus1 ( void ) [protected, inherited]

$a_{n+1}=\sum_{i=1}^{i=n}\frac{1}{i}\$

Warning:: statistic undefined if there are untyped SNPs

Definition at line 1165 of file PolySNP.cc.

double Sequence::PolySNP::b_sub_n ( void ) [protected, inherited]

$b_n=\sum_{i=1}^{i=n-1}\frac{1}{i^2}\$

Warning:: statistic undefined if there are untyped SNPs

Definition at line 1182 of file PolySNP.cc.

double Sequence::PolySNP::b_sub_n_plus1 ( void ) [protected, inherited]

$b_n=\sum_{i=1}^{i=n}\frac{1}{i^2}\$

Warning:: statistic undefined if there are untyped SNPs

Author:: Joshua Shapiro

Definition at line 1197 of file PolySNP.cc.

double Sequence::PolySNP::c_sub_n ( void ) [protected, inherited]

$c_n=\left\{\begin{array}{cl} 1 , & when\ n = 2 \\ \frac{2 \times (n \times a_n - 2 \times (n-1))}{(n-1) \times (n-2)}, & when\ n > 2 \\ \end{array}\right.\$

Warning:: statistic undefined if there are untyped SNPs

Definition at line 1213 of file PolySNP.cc.

double Sequence::PolySNP::d_sub_n ( void ) [protected, inherited]

$\ d_n=\frac{2}{n-1} \times (1.5 - \frac{2 \times a_{n+1}}{n-2} - \frac{1}{n})\$

Warning:: statistic undefined if there are untyped SNPs

Definition at line 1239 of file PolySNP.cc.

double Sequence::PolySNP::DandVH ( void ) [inherited]

To check if two sequences are unique, Sequence::Comparisons::Different is used, which does not allow missing data to result in 2 sequences being considered different (as they would be if you simply used thestd::string comparison operators == or !=)

Returns:: the haplotype diversity of the data.

Examples:: bottleneck.cc.

Definition at line 1256 of file PolySNP.cc.

unsigned Sequence::PolySNP::DandVK ( void ) [inherited]

To check if two sequences are unique, Sequence::Comparisons::Different is used, which does not allow missing data to result in 2 sequences being considered different (as they would be if you simply used the std::string comparison operators == or !=)

Returns:: number of haplotypes in the sample

Definition at line 1273 of file PolySNP.cc.

void Sequence::PolySNP::DepaulisVeuilleStatistics ( void ) [protected, inherited]

Calculate the number of haplotypes in the sample, and haplotype diversity. Unlike Depaulis and Veuille's original paper, this routine uses an unbiased calculation of haplotype diversity (i.e. divide by n choose 2).
To check if two sequences are unique, Sequence::Comparisons::Different is used, which does not allow missing data to result in 2 sequences being considered different (as they would be if you simply used the std::string comparison operators == or !=)

Definition at line 753 of file PolySNP.cc.

std::vector< std::vector< double > > Sequence::PolySNP::Disequilibrium	(	const unsigned &	mincount = `1`,
		const double &	max_marker_distance = `std::numeric_limits<double>::max()`
	)			`[inherited]`

Returns:: A vector of statistics related to LD and distance in the sample. An empty vector is returned if there are < 2 polymorphic sites in the sample. See the documentation for Recombination::Disequilibrium for a description of the return vector.

Parameters:

mincount

a frequency filter. A polymorphism must be present at least mincount times in the data

Note:: For D and D', the 11 gamete is defined as follows: If no outgroup is present, it refers to the genotype of minor alleles at both sites. If there is an outgroup, it is based on the genotype of derived alleles at both sites.

Definition at line 1420 of file PolySNP.cc.

double Sequence::PolySIM::Dnominator ( void ) [virtual]

Warning:: statistic undefined if there are untyped SNPs

Returns:: Denominator of Tajima's D, or nan if there are no polymorphic sites

Reimplemented from Sequence::PolySNP.

Definition at line 181 of file PolySIM.cc.

double Sequence::PolySIM::FuLiD ( void ) [virtual]

Returns:: The Fu and Li (1993) D statistic, or nan if there are no polymorphic sites.

Note:: For sequence data, an outgroup is required. This requirement is checked by assert()

Warning:: statistic undefined if there are untyped SNPs

Reimplemented from Sequence::PolySNP.

Examples:: msstats.cc.

Definition at line 309 of file PolySIM.cc.

double Sequence::PolySIM::FuLiDStar ( void ) [virtual]

Warning:: statistic undefined if there are untyped SNPs

Returns:: Fu and Li (1993) D*, or nan if there are no polymorphic sites

Reimplemented from Sequence::PolySNP.

Examples:: msstats.cc.

Definition at line 357 of file PolySIM.cc.

double Sequence::PolySIM::FuLiF ( void ) [virtual]

Returns:: Fu and Li (1993) F statistic, or nan if there are no polymorphic sites

Note:: For sequence data, an outgroup is required, else undefined

Warning:: statistic undefined if there are untyped SNPs

Reimplemented from Sequence::PolySNP.

Examples:: msstats.cc.

Definition at line 329 of file PolySIM.cc.

double Sequence::PolySIM::FuLiFStar ( void ) [virtual]

Fu and Li (1993) F* statistic. Incorporates correction from Simonsen et al. (1995) Genetics 141: 413, eqn A5.

Warning:: statistic undefined if there are untyped SNPs

Returns:: Fu and Li (1993) F* statistic, or nan if there are no polymorphic sites

Reimplemented from Sequence::PolySNP.

Examples:: msstats.cc.

Definition at line 384 of file PolySIM.cc.

double Sequence::PolySIM::Hprime ( bool likeThorntonAndolfatto = false ) [virtual]

Redefinition of PolySNP::Hprime

Author:: Joshua Shapiro

Reimplemented from Sequence::PolySNP.

Definition at line 142 of file PolySIM.cc.

double Sequence::PolySNP::HudsonsC ( void ) [inherited]

Returns:: Hudson's (1987) estimator of $\rho=4Nc$ , an estimator of the population recombination rate that depends on the variance of the site frequencies. The calculation is made by a call to Recombination::HudsonsC

Note:: Will return nan if there are no polymorphic sites

Definition at line 1290 of file PolySNP.cc.

int Sequence::PolySIM::HudsonsHaplotypeTest	(	int	subsize,
		int	subss
	)

From Hudson et al (1994) on polymorphism at sod. For simulated data only. The function returns a 1 if the number of polymorphisms in a randomly generated subsample of the data is less than or equal to subss, 0 otherwise.

Parameters:

	subsize	the size of the subsample
	subss	the number of segregating sites in the subsample

Author:: Dick Hudson; Kevin Thornton

Definition at line 202 of file PolySIM.cc.

unsigned Sequence::PolySIM::Minrec ( void ) [virtual]

Returns:: the minimum number of recombination events observed in the sample (Hudson and Kaplan 1985). Will return SEQMAXUNSIGNED if there are < 2 segregating sites.

Note:: code is a modification of that provided by Jeff Wall

Reimplemented from Sequence::PolySNP.

Definition at line 476 of file PolySIM.cc.

unsigned Sequence::PolySIM::NumExternalMutations ( void ) [virtual]

similar to num singletons, but it assumes strict ancestral vs. derived in the data-> i.e. for the infinite-sites case, 0 is ancestral, 1 is derived (as in the case of coalescent simulations). note that Sequence does put 1 as the derived state, if you have an outgroup, so this is the routine to use.

Returns:: the number of derived alleles at frequency 1

Reimplemented from Sequence::PolySNP.

Definition at line 452 of file PolySIM.cc.

unsigned Sequence::PolySIM::NumMutations ( void ) [virtual]

Returns:: number of mutations in the sample

Reimplemented from Sequence::PolySNP.

Definition at line 412 of file PolySIM.cc.

unsigned Sequence::PolySNP::NumPoly ( void ) [inherited]

Returns:: the number of polymorphic (segregating) sites in data

Examples:: msstats.cc.

Definition at line 547 of file PolySNP.cc.

unsigned Sequence::PolySIM::NumSingletons ( void ) [virtual]

A version optimized for simulated data where character states take on the values 0 or 1.

Returns:: number of sites where there is a mutation at frequency 1 in the sample

Reimplemented from Sequence::PolySNP.

Definition at line 423 of file PolySIM.cc.

double Sequence::PolySNP::SamplingVarPi ( void ) [inherited]

Component of variance of mean pairwise differences from sampling. Tajima in Takahata/Clark book, (15)

Warning:: statistic undefined if there are untyped SNPs

Definition at line 976 of file PolySNP.cc.

double Sequence::PolySNP::StochasticVarPi ( void ) [inherited]

Stochastic variance of mean pairwise differences. Tajima in Takahata/Clark book, (14).

Warning:: statistic undefined if there are untyped SNPs

Definition at line 962 of file PolySNP.cc.

double Sequence::PolySIM::TajimasD ( void ) [virtual]

A common summary of the site frequency spectrum. Proportional to $\widehat\theta_\pi-\widehat\theta_W$ . This routine does calculate the denominator of the test statistic.

Warning:: statistic undefined if there are untyped SNPs

Returns:: Tajima's D, or nan if there are no polymorphic sites

Reimplemented from Sequence::PolySNP.

Examples:: bottleneck.cc, and msstats.cc.

Definition at line 133 of file PolySIM.cc.

double Sequence::PolySIM::ThetaH ( void ) [virtual]

For simulated data, where 0 is ancenstral, 1 derived.
A simpler version of PolySIM::ThetaH (const Sequence::PolyTable * data, bool haveOutgroup = 0, unsigned outgroup = 0)

Reimplemented from Sequence::PolySNP.

Examples:: msstats.cc.

Definition at line 88 of file PolySIM.cc.

double Sequence::PolySIM::ThetaL ( void ) [virtual]

For simulated data, where 0 is ancenstral, 1 derived.
A simpler version of PolySIM::ThetaL()

Author:: Joshua Shapiro

Reimplemented from Sequence::PolySNP.

Definition at line 106 of file PolySIM.cc.

double Sequence::PolySIM::ThetaPi ( void ) [virtual]

For simulated data, assuming 0 is ancenstral, 1 derived.
A simpler version of PolySNP::ThetaPi

Reimplemented from Sequence::PolySNP.

Examples:: bottleneck.cc, and msstats.cc.

Definition at line 55 of file PolySIM.cc.

double Sequence::PolySIM::ThetaW ( void ) [virtual]

For coalescent simulation data, the number of segregating sites equals the number of mutations on the tree (under the infinite sites model.

Reimplemented from Sequence::PolySNP.

Examples:: msstats.cc.

Definition at line 76 of file PolySIM.cc.

double Sequence::PolySNP::VarPi ( void ) [inherited]

Total variance of mean pairwise differences. Tajima in Takahata/Clark book, (13).

Warning:: statistic undefined if there are untyped SNPs

Definition at line 948 of file PolySNP.cc.

double Sequence::PolySNP::VarThetaW ( void ) [inherited]

Returns:: Variance of Watterson's Theta (ThetaW()).

Warning:: statistic undefined if there are untyped SNPs

Definition at line 993 of file PolySNP.cc.

double Sequence::PolySIM::WallsB ( void ) [virtual]

Returns:: Wall's B Statistic. Wall, J. (1999) Genetical Research 74, pp 65-79

Author:: Kevin Thornton

Reimplemented from Sequence::PolySNP.

Definition at line 633 of file PolySIM.cc.

unsigned Sequence::PolySIM::WallsBprime ( void ) [virtual]

Returns:: Wall's B' Statistic. Wall, J. (1999) Genetical Research 74, pp 65-79

Author:: Kevin Thornton

Reimplemented from Sequence::PolySNP.

Definition at line 639 of file PolySIM.cc.

double Sequence::PolySIM::WallsQ ( void ) [virtual]

Returns:: Wall's Q Statistic. Wall, J. (1999) Genetical Research 74, pp 65-79

Author:: Kevin Thornton

Reimplemented from Sequence::PolySNP.

Definition at line 645 of file PolySIM.cc.

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

Sequence::PolySIM Class Reference [Analysis of molecular population genetic data]

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Sequence::PolySIM Class Reference
[Analysis of molecular population genetic data]