MultilocusGenotypeStatistics.h

Go to the documentation of this file.

// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef _MULTILOCUSGENOTYPESTATISTICS_H_
#define _MULTILOCUSGENOTYPESTATISTICS_H_
 
// From STL
#include <string>
#include <vector>
#include <map>
#include <set>
#include <memory>
 
#include <Bpp/Exceptions.h>
 
// From bpp-seq
#include <Bpp/Seq/DistanceMatrix.h>
 
// From bpp-popgen
#include "PolymorphismMultiGContainer.h"
#include "MultilocusGenotype.h"
#include "GeneralExceptions.h"
 
namespace bpp
{
class MultilocusGenotypeStatistics
{
public:
  struct VarComp
  {
    double a;
    double b;
    double c;
  };
 
  struct Fstats
  {
    double Fit;
    double Fst;
    double Fis;
  };
 
  struct PermResults
  {
    double statistic;
    double percentSup;
    double percentInf;
  };
 
  static std::vector<size_t> getAllelesIdsForGroups(
      const PolymorphismMultiGContainer& pmgc,
      size_t locusPosition,
      const std::set<size_t>& groups);
 
  static size_t countGametesForGroups(
      const PolymorphismMultiGContainer& pmgc,
      size_t locusPosition,
      const std::set<size_t>& groups);
 
  static std::map<size_t, size_t> getAllelesMapForGroups(
      const PolymorphismMultiGContainer& pmgc,
      size_t locusPosition,
      const std::set<size_t>& groups);
 
  static std::map<size_t, double> getAllelesFrqForGroups(
      const PolymorphismMultiGContainer& pmgc,
      size_t locusPosition,
      const std::set<size_t>& groups);
 
  static size_t countNonMissingForGroups(
      const PolymorphismMultiGContainer& pmgc,
      size_t locusPosition,
      const std::set<size_t>& groups);
 
  static size_t countBiAllelicForGroups(
      const PolymorphismMultiGContainer& pmgc,
      size_t locusPosition,
      const std::set<size_t>& groups);
 
  static std::map<size_t, size_t> countHeterozygousForGroups(
      const PolymorphismMultiGContainer& pmgc,
      size_t locusPosition,
      const std::set<size_t>& groups);
 
  static std::map<size_t, double> getHeterozygousFrqForGroups(
      const PolymorphismMultiGContainer& pmgc,
      size_t locusPosition,
      const std::set<size_t>& groups);
 
  static double getHobsForGroups(
      const PolymorphismMultiGContainer& pmgc,
      size_t locusPosition,
      const std::set<size_t>& groups);
 
  static double getHexpForGroups(
      const PolymorphismMultiGContainer& pmgc,
      size_t locusPosition,
      const std::set<size_t>& groups);
 
  static double getHnbForGroups(
      const PolymorphismMultiGContainer& pmgc,
      size_t locusPosition,
      const std::set<size_t>& groups);
 
  static double getDnei72(
      const PolymorphismMultiGContainer& pmgc,
      std::vector<size_t> locusPositions,
      size_t grp1,
      size_t grp2);
 
  static double getDnei78(
      const PolymorphismMultiGContainer& pmgc,
      std::vector<size_t> locusPositions,
      size_t grp1,
      size_t grp2);
 
  static std::map<size_t, Fstats> getAllelesFstats(
      const PolymorphismMultiGContainer& pmgc,
      size_t locusPosition,
      const std::set<size_t>& groups);
 
  static std::map<size_t, double> getAllelesFit(
      const PolymorphismMultiGContainer& pmgc,
      size_t locusPosition,
      const std::set<size_t>& groups);
 
  static std::map<size_t, double> getAllelesFst(
      const PolymorphismMultiGContainer& pmgc,
      size_t locusPosition,
      const std::set<size_t>& groups);
 
  static std::map<size_t, double> getAllelesFis(
      const PolymorphismMultiGContainer& pmgc,
      size_t locusPosition,
      const std::set<size_t>& groups);
 
  static std::map<size_t, VarComp> getVarianceComponents(
      const PolymorphismMultiGContainer& pmgc,
      size_t locusPosition,
      const std::set<size_t>& groups);
 
  static double getWCMultilocusFst(
      const PolymorphismMultiGContainer& pmgc,
      std::vector<size_t> locusPositions,
      const std::set<size_t>& groups);
 
  static double getWCMultilocusFis(
      const PolymorphismMultiGContainer& pmgc,
      std::vector<size_t> locusPositions,
      const std::set<size_t>& groups);
 
  static PermResults getWCMultilocusFstAndPerm(
      const PolymorphismMultiGContainer& pmgc,
      std::vector<size_t> locusPositions,
      std::set<size_t> groups,
      unsigned int nb_perm);
 
  static PermResults getWCMultilocusFisAndPerm(
      const PolymorphismMultiGContainer& pmgc,
      std::vector<size_t> locusPositions,
      std::set<size_t> groups,
      unsigned int nbPerm);
 
 
  static double getRHMultilocusFst(
      const PolymorphismMultiGContainer& pmgc,
      std::vector<size_t> locusPositions,
      const std::set<size_t>& groups);
 
  static std::unique_ptr<DistanceMatrix> getDistanceMatrix(
      const PolymorphismMultiGContainer& pmgc,
      std::vector<size_t> locusPositions,
      const std::set<size_t>& groups,
      std::string distance_method);
};
} // end of namespace bpp;
 
#endif // _MULTILOCUSGENOTYPESTATISTICS_H_