Methods dealing with recombination. More...

Functions
double	HudsonsC (const Sequence::PolyTable *data, const bool &haveOutgroup, const unsigned &outgroup) __attribute__((deprecated))

std::vector< PairwiseLDstats >	Disequilibrium (const Sequence::PolyTable *data, const bool &haveOutgroup=false, const unsigned &outgroup=0, const unsigned &mincount=1, const double max_distance=std::numeric_limits< double >::max()) __attribute__((deprecated))
	Calculate pairwise LD for a Sequence::PolyTable. More...

PairwiseLDstats	PairwiseLD (const Sequence::PolyTable *data, unsigned i, unsigned j, const bool &haveOutgroup=false, const unsigned &outgroup=0, const unsigned &mincount=1, const double max_distance=std::numeric_limits< double >::max()) __attribute__((deprecated))

Variables
const double	CMAX = 10000

Detailed Description

Methods dealing with recombination.

This namespace exists primarily so that the file Poly.cc (which defines Sequence::Poly) does not get too large. The routines defined in this namespace all have to do with properties of the association between sites. Current methods implemented are:
1.) Recombination::HudsonsC, which calculates Hudson's C, aka $\rho_{87}$

2.) Recombination::Disequilibrium, which calculated several measures of LD for all pairs of sites, and implements a frequency filter to remove low-frequency variants if desired.

Function Documentation

◆ Disequilibrium()

std::vector< PairwiseLDstats > Sequence::Recombination::Disequilibrium	(	const Sequence::PolyTable *	data,
		const bool &	haveOutgroup = `false`,
		const unsigned &	outgroup = `0`,
		const unsigned &	mincount = `1`,
		const double	max_distance = `std::numeric_limits<double>::max()`
	)

Calculate pairwise LD for a Sequence::PolyTable.

This function is threaded (see threads) and implemented in terms of Sequence::PairwiseLD.

Parameters

data	A Sequence::PolyTable
haveOutgroup	A boolean
outgroup.	If haveOutgroup is true, then this is the index of the outgroup sequence in data
mincount	Minimum sample count to include a mutation. E.g., 2 = exclude singletons, etc.
max_distance	Do not include sites > this value apart

Returns: A std::vector of Sequence::PairwiseLDstats

Definition at line 353 of file Recombination.cc.

◆ HudsonsC()

double Sequence::Recombination::HudsonsC	(	const Sequence::PolyTable *	data,
		const bool &	haveOutgroup,
		const unsigned &	outgroup
	)

Returns Hudson's (1987) Genetical Research 50:245-250 moment estimator of the population recombination rate. Please note that the properties of this estimator are not ideal, and one should prefer Hudson (2001) Genetics 159: 1805-1817 or McVean et al. (2002) Genetics 160: 1231-1241

Definition at line 329 of file Recombination.cc.

◆ PairwiseLD()

PairwiseLDstats Sequence::Recombination::PairwiseLD	(	const Sequence::PolyTable *	data,
		unsigned	i,
		unsigned	j,
		const bool &	haveOutgroup = `false`,
		const unsigned &	outgroup = `0`,
		const unsigned &	mincount = `1`,
		const double	max_distance = `std::numeric_limits<double>::max()`
	)

Calculates LD statistics for sites i and j, where j>1.

Parameters

data	The polymorphism data
i	Index for site in data
j	Index for site in data
haveOutgroup	true if data contains an outgroup, false otherwise
outgroup	the index of the outgroup in data haveOutgroup is true
mincount	the minimum sample frequency to include
max_distance	max distance between markers (on scale in which positions in data are stored) for inclusion

Returns: Sequence::PairwiseLDstats

Definition at line 377 of file Recombination.cc.

Variable Documentation

◆ CMAX

const double Sequence::Recombination::CMAX = 10000

The max value that can be taken by $\rho_{87}$

Definition at line 48 of file Recombination.cc.

Functions