Summary statistics and other analysis of Sequence::VariantMatrixSee Tutorial/overview. More...

Namespaces
	Sequence::Recombination
	Methods dealing with recombination.

Classes
struct	Sequence::PairwiseLDstats
	Pairwise linkage disequilibrium (LD) stats . More...

struct	Sequence::AlleleCounts

struct	Sequence::GarudStats

struct	Sequence::nSLiHS

class	Sequence::PolySIM
	Analysis of coalescent simulation data. More...

class	Sequence::PolySNP
	Molecular population genetic analysis. More...

class	Sequence::PolyTableSlice< T >
	A container class for "sliding windows" along a polymorphism table. More...

class	Sequence::FST
	analysis of population structure using $F_{ST}$ More...

Functions
std::pair< double, double >	Sequence::nSL (const std::size_t &core, const SimData &d, const std::unordered_map< double, double > &gmap=std::unordered_map< double, double >()) __attribute__((deprecated))

template<typename F >
void	Sequence::sstats_algo::aggregate_sites (const VariantMatrix &m, const F &f, const std::int8_t refstate)

template<typename F >
void	Sequence::sstats_algo::aggregate_sites (const VariantMatrix &m, const F &f, const std::vector< std::int8_t > &refstates)

std::vector< AlleleCounts >	Sequence::allele_counts (const AlleleCountMatrix &m)
	Count number of alleles at each site. More...

std::vector< AlleleCounts >	Sequence::non_reference_allele_counts (const AlleleCountMatrix &m, const std::int8_t refstate)
	Count number of non-reference alleles at each site. More...

std::vector< AlleleCounts >	Sequence::non_reference_allele_counts (const AlleleCountMatrix &m, const std::vector< std::int8_t > &refstates)
	Count number of non-reference alleles at each site. More...

double	Sequence::tajd (const AlleleCountMatrix &ac)
	Tajima's D. More...

double	Sequence::hprime (const AlleleCountMatrix &ac, const std::int8_t refstate)

double	Sequence::hprime (const AlleleCountMatrix &m, const std::vector< std::int8_t > &refstates)

double	Sequence::faywuh (const AlleleCountMatrix &ac, const std::int8_t refstate)
	Fay and Wu's H. More...

double	Sequence::faywuh (const AlleleCountMatrix &ac, const std::vector< std::int8_t > &refstates)
	Fay and Wu's H. More...

std::vector< std::int32_t >	Sequence::difference_matrix (const VariantMatrix &m)
	Calculate number of differences between all samples. More...

std::vector< std::int32_t >	Sequence::label_haplotypes (const VariantMatrix &m)
	Assign a unique label to each haplotype. More...

std::int32_t	Sequence::number_of_haplotypes (const VariantMatrix &m)
	Calculate the number of haplotypes in a sample. More...

double	Sequence::haplotype_diversity (const VariantMatrix &m)
	Calculate the haplotype diversity of a sample. More...

std::int32_t	Sequence::rmin (const VariantMatrix &m)

std::uint32_t	Sequence::nvariable_sites (const AlleleCountMatrix &m)
	Number of polymorphic sites. More...

std::uint32_t	Sequence::nbiallelic_sites (const AlleleCountMatrix &m)
	Number of bi-allelic sites. More...

std::uint32_t	Sequence::total_number_of_mutations (const AlleleCountMatrix &m)
	Total number of mutations in the sample. More...

double	Sequence::thetah (const AlleleCountMatrix &ac, const std::int8_t refstate)
	Fay and Wu's $\hat\theta_H$ . More...

double	Sequence::thetah (const AlleleCountMatrix &m, const std::vector< std::int8_t > &refstates)
	Fay and Wu's $\hat\theta_H$ . More...

double	Sequence::thetal (const AlleleCountMatrix &ac, const std::int8_t refstate)
	Zeng et al. $\hat\theta_L$ . More...

double	Sequence::thetal (const AlleleCountMatrix &m, const std::vector< std::int8_t > &refstates)
	Zeng et al. $\hat\theta_L$ . More...

double	Sequence::thetapi (const AlleleCountMatrix &ac)
	Mean pairwise differences. More...

double	Sequence::thetaw (const AlleleCountMatrix &ac)
	Watterson's theta. More...

nSLiHS	Sequence::nsl (const VariantMatrix &m, const std::size_t core, const std::int8_t refstate)
	nSL and iHS statistics More...

Detailed Description

Summary statistics and other analysis of Sequence::VariantMatrix

See Tutorial/overview.

Function Documentation

◆ aggregate_sites() [1/2]

template<typename F >

void Sequence::sstats_algo::aggregate_sites	(	const VariantMatrix &	m,
		const F &	f,
		const std::int8_t	refstate
	)

inline

Helper algorithm for implementing summary statistics.

Several common summary statistics are combinations of others. Examples include Tajima's D, Fay and Wu's H, etc.. If we take D as an example, it is tempting to use existing functions, such as Sequence::thetapi and Sequence::thetaw, as intermediate steps. However, doing so goes over the data multiple times.

Fortunately, these statistics are often easy enough to implement that we could calculate pi and Watterson's theta in one loop. This function helps you do that.

Parameters

m	A VariantMatrix
f	A function taking a const StateCounts & and returning nothing.
refstate	The reference state.

This function loops over m.nsites and passes the state counts on to the aggregator function f.

See the implementation of Sequence::tajd for an example.

Definition at line 18 of file algorithm.hpp.

◆ aggregate_sites() [2/2]

template<typename F >

void Sequence::sstats_algo::aggregate_sites	(	const VariantMatrix &	m,
		const F &	f,
		const std::vector< std::int8_t > &	refstates
	)

inline

Helper algorithm for implementing summary statistics.

Several common summary statistics are combinations of others. Examples include Tajima's D, Fay and Wu's H, etc.. If we take D as an example, it is tempting to use existing functions, such as Sequence::thetapi and Sequence::thetaw, as intermediate steps. However, doing so goes over the data multiple times.

Fortunately, these statistics are often easy enough to implement that we could calculate pi and Watterson's theta in one loop. This function helps you do that.

Parameters

m	A VariantMatrix
f	A function taking a const StateCounts & and returning nothing.
refstates	Vector of reference states

This function loops over m.nsites and passes the state counts on to the aggregator function f.

See the implementation of Sequence::hprime for an example.

Definition at line 56 of file algorithm.hpp.

◆ allele_counts()

count_type Sequence::allele_counts ( const AlleleCountMatrix & m )

Count number of alleles at each site.

Parameters

m	An AlleleCountMatrix

Definition at line 50 of file allele_counts.cc.

◆ difference_matrix()

std::vector< std::int32_t > Sequence::difference_matrix ( const VariantMatrix & m )

Calculate number of differences between all samples.

Parameters

m	A VariantMatrix

Returns: std::vector<std::int32_t>

For $n$ samples in m, the output contains $n \choose 2$ elements. More concretely, the elements are populated according to:

for(int i=0; i < m.nsam - 1; ++i)
{
     for(int j=i+1 ; j < m.nsam ; ++j)
     {
         //diffs[i] = number of diffs between sample i and j      
     }
}    

Missing data to not contribute to differences between sequences. Thus, low-quality data may lead to uninformative return values.

Included via Sequence/summstats.hpp or Sequence/summstats/classics.hpp

Definition at line 15 of file haplotype_statistics.cc.

◆ faywuh() [1/2]

double Sequence::faywuh	(	const AlleleCountMatrix &	ac,
		const std::int8_t	refstate
	)

Fay and Wu's H.

Parameters

m	An AlleleCountMatrix
refstate	The ancestral state.

Returns: Fay and Wu's H, or nan if m is empty/invariant.

Note: It is an error to consider refstate as anything other than the ancestral state for each site.

This function is included via Sequence/summstats.hpp, Sequence/summstats/classics.hpp Sequence/summstats/thetah.hpp

See [2] for details.

Definition at line 8 of file faywuh.cc.

◆ faywuh() [2/2]

double Sequence::faywuh	(	const AlleleCountMatrix &	ac,
		const std::vector< std::int8_t > &	refstates
	)

Fay and Wu's H.

Parameters

m	An AlleleCountMatrix
refstates	The ancestral state at each site.

Returns: Fay and Wu's H, or nan if m is empty/invariant.

Note: It is an error to consider refstates as anything other than the ancestral state at each site.

This function is included via Sequence/summstats.hpp, or Sequence/summstats/classics.hpp

See [2] for details.

Definition at line 33 of file faywuh.cc.

◆ haplotype_diversity()

double Sequence::haplotype_diversity ( const VariantMatrix & m )

Calculate the haplotype diversity of a sample.

Parameters

m	A VariantMatrix

Returns: Haplotype heterozygosity, a double.

The "haplotype heterozygosity" is calculated by counting haplotype labels (see label_haplotypes).

Note: The value nan is returned if m.nsam == 0. If m contains data, but all sites are invariant, the function returns 0.0. See testClassicSummstatsEmptyVariantMatrix.cc for examples.

Included via Sequence/summstats.hpp or Sequence/summstats/classics.hpp

See [1] for details.

Definition at line 134 of file haplotype_statistics.cc.

◆ hprime() [1/2]

double Sequence::hprime	(	const AlleleCountMatrix &	ac,
		const std::int8_t	refstate
	)

The H' statistic

Parameters

m	An AlleleCountMatrix
refstate	How the ancestral state is encoded.

Returns: H'

Note: nan is returned if m is empty/invariant. It is an error to consider refstate as anything other than the ancestral state.

See [10] for details.

Included via Sequence/summstats.hpp or Sequence/summstats/classics.hpp

Definition at line 45 of file hprime.cc.

◆ hprime() [2/2]

double Sequence::hprime	(	const AlleleCountMatrix &	m,
		const std::vector< std::int8_t > &	refstates
	)

The H' statistic

Parameters

m	An AlleleCountMatrix
refstates	A vector of ancestral states, equal in length to m.sites

Returns: H'

Note: nan is returned if m is empty/invariant. It is an error to consider refstates as anything other than the ancestral state at each site.

See [10] for details.

Included via Sequence/summstats.hpp or Sequence/summstats/classics.hpp

Definition at line 67 of file hprime.cc.

◆ label_haplotypes()

std::vector< std::int32_t > Sequence::label_haplotypes ( const VariantMatrix & m )

Assign a unique label to each haplotype.

Parameters

m	A VariantMatrix

Returns: std::vector<std::int32_t>

If there are $k$ unique samples in m, which represents a sample of size nsam, the return value contains nsam elements whose values are $[0,k)$ for "good" input. Here, "bad" input means that some of the samples consist entirely of missing data. In that case, they are given the label of -1.

This function is implemented via a call to difference_matrix.

Included via Sequence/summstats.hpp or Sequence/summstats/classics.hpp

Definition at line 75 of file haplotype_statistics.cc.

◆ nbiallelic_sites()

std::uint32_t Sequence::nbiallelic_sites ( const AlleleCountMatrix & m )

Number of bi-allelic sites.

Return the number of sites with exactly two non-missing states.

Parameters

m	An AlleleCountMatrix

Returns: std::uint32_t

Definition at line 28 of file nvariablesites.cc.

◆ non_reference_allele_counts() [1/2]

count_type Sequence::non_reference_allele_counts	(	const AlleleCountMatrix &	m,
		const std::int8_t	refstate
	)

Count number of non-reference alleles at each site.

Parameters

m	An AlleleCountMatrix
m	refstate The reference state for all sites.

Definition at line 80 of file allele_counts.cc.

◆ non_reference_allele_counts() [2/2]

count_type Sequence::non_reference_allele_counts	(	const AlleleCountMatrix &	m,
		const std::vector< std::int8_t > &	refstates
	)

Count number of non-reference alleles at each site.

Parameters

m	An AlleleCountMatrix
m	refstate The reference state at each site.

Definition at line 62 of file allele_counts.cc.

◆ nsl()

nSLiHS Sequence::nsl	(	const VariantMatrix &	m,
		const std::size_t	core,
		const std::int8_t	refstate
	)

nSL and iHS statistics

Parameters

m	A VariantMatrix
core	The index of the core site
refstate	The value of the reference/ancestral allelic state

Returns: an nSLiHS object

See nSL_from_ms.cc for example

See [3] for details.

Examples:: nSL_from_ms.cc.

Definition at line 76 of file nsl.cc.

◆ nSL()

pair< double, double > Sequence::nSL	(	const std::size_t &	core,
		const SimData &	d,
		const std::unordered_map< double, double > &	gmap = `std::unordered_map<double, double>()`
	)

The nSL statistic of Ferrer-Admetlla et al. doi: 10.1093/molbev/msu077.

Parameters

core	The index of the "focal/core" SNP
d	An object of type Sequence::SimData
gmap	The positions of every marker in d on the genetic map. If std::unordered_map<double,double>() is passed, iHS is calculated using SNP positions.

Returns: nSL and iHs, with the latter as defined in doi: 10.1093/molbev/msu077.

Note: This routine was validated by comparing to code provided by Ferrer-Admetlla et al.

Warning: The use of 'gmap' is untested.

Definition at line 124 of file nSL.cc.

◆ number_of_haplotypes()

std::int32_t Sequence::number_of_haplotypes ( const VariantMatrix & m )

Calculate the number of haplotypes in a sample.

Parameters

m	A VariantMatrix

Returns: The number of unique elements in the sample, std::int32_t

This returns the number of unique columns in m.

Note: The value -1 is returned if m.nsam == 0. If m contains data, but all sites are invariant, the function returns 1. See testClassicSummstatsEmptyVariantMatrix.cc for examples.

Include via Sequence/summstats.hpp or Sequence/summstats/classics.hpp

See [1] for details.

Definition at line 117 of file haplotype_statistics.cc.

◆ nvariable_sites()

std::uint32_t Sequence::nvariable_sites ( const AlleleCountMatrix & m )

Number of polymorphic sites.

Returns the number of sites with more than one non-missing state

Parameters

m	An AlleleCountMatrix

Returns: std::uint32_t

Definition at line 8 of file nvariablesites.cc.

◆ rmin()

std::int32_t Sequence::rmin ( const VariantMatrix & m )

Hudson and Kaplan's Rmin statistic

Parameters

m	A VariantMatrix

Returns: Rmin, std::int32_t

Included via Sequence/summstats.hpp or Sequence/summstats/classics.hpp

See [5] for details.

Definition at line 11 of file rmin.cc.

◆ tajd()

double Sequence::tajd ( const AlleleCountMatrix & ac )

Tajima's D.

Parameters

m	An AlleleCountMatrix

Returns: Tajima's D

Note: nan is returned if m is empty/invariant.

See [7] for details.

Included via Sequence/summstats.hpp or Sequence/summstats/classics.hpp

Definition at line 9 of file tajd.cc.

◆ thetah() [1/2]

double Sequence::thetah	(	const AlleleCountMatrix &	ac,
		const std::int8_t	refstate
	)

Fay and Wu's $\hat\theta_H$ .

Parameters

m	An AlleleCountMatrix
refstate	The ancestral state

Returns: double

See [2] for details.

Definition at line 117 of file thetah_thetal.cc.

◆ thetah() [2/2]

double Sequence::thetah	(	const AlleleCountMatrix &	m,
		const std::vector< std::int8_t > &	refstates
	)

Fay and Wu's $\hat\theta_H$ .

Parameters

m	a VariantMatrix
refstate	Vector of ancestral states.

Returns: double

See [2] for details.

Definition at line 123 of file thetah_thetal.cc.

◆ thetal() [1/2]

double Sequence::thetal	(	const AlleleCountMatrix &	ac,
		const std::int8_t	refstate
	)

Zeng et al. $\hat\theta_L$ .

Parameters

m	An AlleleCountMatrix
refstate	The ancestral state

Returns: double

See [10] for details.

Definition at line 130 of file thetah_thetal.cc.

◆ thetal() [2/2]

double Sequence::thetal	(	const AlleleCountMatrix &	m,
		const std::vector< std::int8_t > &	refstates
	)

Zeng et al. $\hat\theta_L$ .

Parameters

m	An AlleleCountMatrix
refstate	Vector of ancestral states.

Returns: double

See [10] for details.

Definition at line 136 of file thetah_thetal.cc.

◆ thetapi()

double Sequence::thetapi ( const AlleleCountMatrix & ac )

Mean pairwise differences.

Parameters

m	An AlleleCountMatrix

Returns: Mean pairwise differences

Note: Calcuated as sum over one minus site homozygosity

This function is included via Sequence/summstats.hpp, Sequence/summstats/classics.hpp or Sequence/summstats/thetapi.hpp

See [6] for details.

Definition at line 7 of file thetapi.cc.

◆ thetaw()

double Sequence::thetaw ( const AlleleCountMatrix & ac )

Watterson's theta.

Parameters

m	An AlleleCountMatrix

Returns: Watterson's theta, a double

Note: For a site with states, is added to the number of inferred mutations. In other words, the calculation is based on the total number of mutations.

See [9] for details.

Definition at line 9 of file thetaw.cc.

◆ total_number_of_mutations()

std::uint32_t Sequence::total_number_of_mutations ( const AlleleCountMatrix & m )

Total number of mutations in the sample.

Return $\sum_{i=0}^{i=m.nsites-1}I(i)$ where $I(i)$ is $k_i - 1$ if $k_i$ , the number of states at the $i^{th}$ site, is greater than one, and zero otherwise.

Parameters

m	An AlleleCountMatrix

Returns: std::uint32_t

Definition at line 48 of file nvariablesites.cc.

Namespaces

Classes

Functions

Detailed Description

Function Documentation

◆ aggregate_sites() [1/2]

◆ aggregate_sites() [2/2]

◆ allele_counts()

◆ difference_matrix()

◆ faywuh() [1/2]

◆ faywuh() [2/2]

◆ haplotype_diversity()

◆ hprime() [1/2]

◆ hprime() [2/2]

◆ label_haplotypes()

◆ nbiallelic_sites()

◆ non_reference_allele_counts() [1/2]

◆ non_reference_allele_counts() [2/2]

◆ nsl()

◆ nSL()

◆ number_of_haplotypes()

◆ nvariable_sites()

◆ rmin()

◆ tajd()

◆ thetah() [1/2]

◆ thetah() [2/2]

◆ thetal() [1/2]

◆ thetal() [2/2]

◆ thetapi()

◆ thetaw()

◆ total_number_of_mutations()