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| template<class T > |
| | DNA (Population< T > *pop) |
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| DNA (Population< Humandna > *pop, int tdna) |
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| | DNA (DNA const &a) |
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| | DNA (DNA const &a, DNA const &b) |
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| | DNA (typeDNA *input, int size) |
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| DNA (array_type const &input, int sizeN, int sizeX) |
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| DNA (std::vector< std::vector< typeDNA > > input) |
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| DNA & | operator= (DNA const &) |
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int | get_N () const |
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| int | get_nbXcell () const |
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| int | get_nbS () const |
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| long | poly_sites () const |
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| double | prop_poly_sites () const |
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| double | mean_pw_diff () const |
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| double | theta_waterson () const |
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double | theta_hom () const |
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double | theta_pi () const |
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| int | nb_of_haplotypes () const |
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| DNA | haplotypes () const |
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| std::vector< double > | hap_frequency () const |
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| std::vector< double > | site_frequency (int site) const |
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| double | heterozigosity_hap () const |
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| double | heterozigosity_sites () const |
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| double | Neff (double theta, double mu) const |
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| double | tajima_D () const |
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| std::vector< double > | site_frequency_DNA (int site) const |
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| typeDNA | dist_two (int a, int b) const |
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| void | output_diversity (std::ofstream &) const |
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| void | output_diversity_with_time (std::ofstream &, int Ntheo, int timeG) const |
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| void | output_diversity (std::ofstream &fs, int Ntheo) const |
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| void | output_arlequin (std::string filename) const |
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| void | output_fasta (std::string filename) const |
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std::ostream & | operator<< (std::ostream &, DNA const &) |
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DNA | operator+ (DNA const &, DNA const &) |
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Constructor which creates a DNA instance from a Population instance. It will extract the mtDNA of each individuals and store it in an array.
Constructor which creates a DNA instance from a Population < Humandna > instance. For each individual it will extract the DNA from either the X chromosome (Nuc = 0), the Y chromomosome (Nuc = 1) or the autosomes (Nuc = 2).
| DNA::DNA |
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DNA const & |
a | ) |
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| DNA::DNA |
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DNA const & |
a, |
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DNA const & |
b |
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Merger of two DNA instance, it concatenates both genetic samples in the same array.
| DNA::DNA |
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typeDNA * |
input, |
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int |
size |
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Constructor directly from an array of DNA sequences.
| typeDNA DNA::dist_two |
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int |
a, |
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int |
b |
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Returns the Hamming distance (number of of different nucleotides) between two sequences.
| int DNA::get_nbS |
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const |
Returns the number of polymorphic sites in the whole sample.
| int DNA::get_nbXcell |
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const |
Returns the number of cell taken by a sequence in the big array. It is the number of sites per sequence divided by 32.
| vector< double > DNA::hap_frequency |
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const |
Returns an array with the frequency of each haplotype found in the sample. The size of this array is the number of haplotypes.
| DNA DNA::haplotypes |
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const |
Returns an array containing all the haplotypes found in the sample.
| double DNA::heterozigosity_hap |
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const |
Returns the heterozygosity of the sample computed at the level of haplotypes, i.e. the allele diversity.
| double DNA::heterozigosity_sites |
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const |
Returns the heterozygosity of the sample computed at the level of sites, i.e. the polymorphic diversity, using Nei's formula.
| double DNA::mean_pw_diff |
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const |
Returns the mean pairwise difference of the sample. It is calculated by summing the distance between each pair of sequences and dividing by the number of pair compared.
| int DNA::nb_of_haplotypes |
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const |
Returns the number of haplotypes in the sample
| double DNA::Neff |
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double |
theta, |
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double |
mu |
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Returns effective population size from an estimation of theta and a mutation rate: theta/(2x Mutation rate).
| DNA & DNA::operator= |
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DNA const & |
a | ) |
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| void DNA::output_arlequin |
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std::string |
filename | ) |
const |
Outputs the sample in a file formatted to be piped through the Arlequin program.
| void DNA::output_diversity |
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std::ofstream & |
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const |
Outputs different diversity indices for the sample in a file.
| void DNA::output_diversity |
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std::ofstream & |
fs, |
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int |
Ntheo |
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| const |
Outputs different diversity indices for the sample in a file, along the real population size (which can be different from the sample one).
| void DNA::output_diversity_with_time |
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std::ofstream & |
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int |
Ntheo, |
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int |
timeG |
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| const |
Outputs different diversity indices for the sample in a file, along the real population size (which can be different from the sample one) and the time of sample.
| void DNA::output_fasta |
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std::string |
filename | ) |
const |
Outputs the sequences in a file in Fasta format, to be used by other sofware.
| long DNA::poly_sites |
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const |
Returns the number polymorhpic sites in the sample.
| double DNA::prop_poly_sites |
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const |
Returns the proportion of polymorphic sites in the sample, i.e. number of polymorphic sites over total number of sites.
| vector< double > DNA::site_frequency |
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int |
site | ) |
const |
Returns an array with the frequency of each found nucleotide on the given site. Its size vary with thenumber of present nuclotides.
| vector< double > DNA::site_frequency_DNA |
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int |
site | ) |
const |
Returns an array with the frequency of each found nucleotide on the given site. Its size is always 4.
| double DNA::tajima_D |
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const |
| double DNA::theta_waterson |
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const |
Returns theta Watterson index of diversity, based on the number of polymorphic sites.
| double DNA::theta_hom |
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const |
Returns an estimator of theta based on the homozygosity of the sample.
| double DNA::theta_pi |
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const |
Returns an estimator of theta based on the mean pairwise difference.
The documentation for this class was generated from the following files:
1.8.4
