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//////////////////////////////////////////////////////////////////
// //
// PLINK (c) 2005-2007 Shaun Purcell //
// //
// This file is distributed under the GNU General Public //
// License, Version 2. Please see the file COPYING for more //
// details //
// //
//////////////////////////////////////////////////////////////////
#include <iostream>
#include <iomanip>
#include <fstream>
#include <sstream>
#include <cmath>
#include <vector>
#include <map>
#include <cassert>
#include "plink.h"
#include "options.h"
#include "helper.h"
#include "genogroup.h"
#include "phase.h"
#include "haplowindow.h"
extern ofstream LOG;
using namespace std;
////////////////////////////////////////////////
// Original, single window EM algorithm, without
// genoGrouping -- this is now used for the meta-EM
void HaploPhase::performEM_original()
{
vector_t uc(nh, 0); // unambigous counts
vector_t ac(nh, 0); // ambigous counts
// Count numbers of unambigous haplotypes
// as these stay constant throughout EM
for (int i=0; i<P.n; i++)
{
if (P.sample[i]->founder && include[i])
{
if (!ambig[i])
{
uc[hap1[i][0]]++;
if ( ! (haploid || (X && P.sample[i]->sex)))
uc[hap2[i][0]]++;
}
}
}
//////////////////
// Begin E-M
double sampleLogLikelihood = 0;
for (int j=0; j<= par::haplo_plem_meta_iter; j++)
{
///////////
// E-step
for (int i=0; i<P.n; i++)
{
if (P.sample[i]->founder && include[i])
{
if (ambig[i])
{
double s=0;
// Haploid phases...
if (haploid || (X && P.sample[i]->sex))
{
for (int z=0; z<hap1[i].size(); z++)
{
pp[i][z] = f[hap1[i][z]];
s += pp[i][z];
}
}
else // ... or diploid
{
for (int z=0; z<hap1[i].size(); z++)
{
pp[i][z] = f[hap1[i][z]] * f[hap2[i][z]];
if (hap1[i][z] != hap2[i][z])
pp[i][z] *= 2;
s += pp[i][z];
}
}
for (int z=0; z<hap1[i].size(); z++)
pp[i][z] /= s;
}
}
}
///////////
// M-step
// unambiguous counts
for (int h=0; h<nh; h++)
f[h] = uc[h];
// then add the fractional ones
for (int i=0; i<P.n; i++)
if (P.sample[i]->founder && include[i])
if (ambig[i])
{
if (haploid || (X && P.sample[i]->sex))
{
for (int z=0; z<hap1[i].size(); z++)
f[hap1[i][z]] += pp[i][z];
}
else
for (int z=0; z<hap1[i].size(); z++)
{
f[hap1[i][z]] += pp[i][z];
f[hap2[i][z]] += pp[i][z];
}
}
// validN is the total number of *chromosomes*
for (int h=0; h<nh; h++)
f[h] /= (double)validN;
///////////////////////
// Update likelihood
if (j % par::haplo_plem_meta_likelihood_iter == 0)
{
double lnl = 0;
for (int i=0; i<P.n; i++)
{
if (P.sample[i]->founder && include[i])
{
double lk = 0;
if (haploid || (X && P.sample[i]->sex))
{
for (int z=0; z<hap1[i].size(); z++)
lk += f[hap1[i][z]];
}
else
for (int z=0; z<hap1[i].size(); z++)
{
lk += f[hap1[i][z]] * f[hap2[i][z]];
if (hap1[i][z] != hap2[i][z])
lk += f[hap1[i][z]] * f[hap2[i][z]];
}
lnl -= log(lk);
}
}
if (j > 0 &&
sampleLogLikelihood - lnl < par::haplo_plem_meta_tol )
{
break;
}
sampleLogLikelihood = lnl;
}
}
}
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