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haplohelper.cpp
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//////////////////////////////////////////////////////////////////
// //
// PLINK (c) 2005-2009 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 <assert.h>
#include "plink.h"
#include "options.h"
#include "phase.h"
#include "helper.h"
#include "genogroup.h"
#include "haplowindow.h"
extern ofstream LOG;
using namespace std;
string HaploPhase::haplotypeName(int h)
{
string str;
for (int s=0; s<ns; s++)
{
string a1 = P.locus[S[s]]->allele1;
string a2 = P.locus[S[s]]->allele2;
if ( a1 == "" ) a1 = "X";
if ( a2 == "" ) a2 = "X";
if (h == -1)
str += "-"; // haploid gap
else if (hap[h][s])
str += a1;
else
str += a2;
}
return str;
}
void HaploPhase::imputeAllHaplotypes()
{
///////////////////////////////////////////////
// Impute missing SNPs -- create a new datafile
// Imputation rules:
// Missing predictor allele -> missing haplotype
// P(H|G) < 0.8 (default) -> missing haplotype
// Make space to new, imputed haplotype calls
new_one.resize(P.n);
new_two.resize(P.n);
/////////////////////////////////
// Phase all specified haplotypes
phaseAllHaplotypes(true,*P.pperm);
///////////////////////////
// Write new PED file
P.printLOG("Imputing genotypes with P(H|G) threshold of " + dbl2str( par::hap_post_prob ) + "\n\n");
string filename = par::output_file_name + ".impute.ped";
P.printLOG("Writing imputed ped file to [ " + filename + " ] \n");
ofstream PED(filename.c_str(), ios::out);
PED.clear();
for (int i=0; i<P.n; i++)
{
Individual * person = P.sample[i];
PED << person->fid<< " "<< person->iid<< " "<< person->pat<< " "
<< person->mat<< " "<< person->sexcode<< " ";
if (par::bt)
PED << (int)person->phenotype;
else
PED << person->phenotype;
for (int l=0; l<new_one[i].size(); l++)
{
if ( (!new_one[i][l]) && (!new_two[i][l]))
PED << par::recode_delimit<< actual_map[l]->allele1<< " "
<< actual_map[l]->allele1;
else if ( (!new_one[i][l]) && new_two[i][l])
PED << par::recode_delimit<< actual_map[l]->allele1<< " "
<< actual_map[l]->allele2;
else if (new_one[i][l] && new_two[i][l])
PED << par::recode_delimit<< actual_map[l]->allele2<< " "
<< actual_map[l]->allele2;
else
PED << par::recode_delimit<< par::missing_genotype << " "
<< par::missing_genotype;
}
PED << "\n";
}
PED.close();
//////////////////
// Write new map
filename = par::output_file_name + ".impute.map";
P.printLOG("Writing imputed map file to [ " + filename + " ] \n");
ofstream MAP(filename.c_str(), ios::out);
MAP.clear();
for (int l=0; l < actual_map.size(); l++)
{
MAP << chromosomeName(actual_map[l]->chr) << "\t"
<< actual_map[l]->name<< "\t"
<< actual_map[l]->pos<< "\t"
<< actual_map[l]->bp<< "\n";
}
MAP.close();
}
void HaploPhase::calculateHaplotypeFrequencies()
{
string f = par::output_file_name + ".frq.hap";
if (par::display_hap_freqs)
{
P.printLOG("Writing haplotype frequencies to [ " + f + " ]\n");
HFRQ.open(f.c_str(), ios::out);
HFRQ.precision(4);
HFRQ << setw(10) << "LOCUS"<< " "<< setw(12) << "HAPLOTYPE"<< " "
<< setw(10) << "F"<< "\n";
}
// Phase all SNPs (with frequency flag set, this routine
// will write haplotype frequencies to HFRQ
P.haplo->phaseAllHaplotypes(true,*P.pperm);
if (par::display_hap_freqs)
HFRQ.close();
// So we do not re-write them
par::display_hap_freqs = false;
}
void HaploPhase::imputeThisHaplotype(int l)
{
////////////////////////////////////////////////////
// Impute for all individiuals, if common haplotype
double w = 0;
double c = 0;
if (testHaplotypeFreq() >= par::min_hf &&
testHaplotypeFreq() <= par::max_hf )
{
for (int i=0; i<P.n; i++)
{
bool b1, b2;
// Haplotype-weighting
double t = imputeHaplotypes(i, b1, b2);
if (t>=0)
{
w += t;
c++;
};
// And set new imputed genotypes
new_one[i].push_back(b1);
new_two[i].push_back(b2);
}
/////////////////////////////////////////////
// Add to map of actually imputed haplotypes
Locus * loc = new Locus;
loc->chr = new_map[l]->chr;
loc->name = hname+"_"+haplotypeName(test_hap)+"_";
loc->bp = new_map[l]->bp;
loc->pos = new_map[l]->pos;
loc->allele1 = new_map[l]->allele1;
loc->allele2 = new_map[l]->allele2;
actual_map.push_back( loc );
}
}
/////////////////////////////////////////////
// Legacy function: now redundant
void HaploPhase::enumerateAllPhases()
{
// Note: this function is no longer called
// For individuals w/out parents: make a list of all possible
// phases. Note: currently, we do not use this (i.e. we always
// require father and mother to be 'observed' (i.e. genotyped and
// adequately phased).
// Also note: issue with representing heterozygote haplotypes twice
// in list: previously we did not, but we now change this (seeing as
// it is never used in any case...)
// Also: now we build separate lists for diploid and haploid
// chromosomes, not that we use either.
// Diploid possible phases
if ( !haploid )
{
for (int h1=0; h1<nh; h1++)
for (int h2=0; h2<nh; h2++)
{
double freq = f[h1] * f[h2];
if (h1!=h2)
freq *= 2;
if (freq >= par::hap_min_phase_prob )
{
ph_freq.push_back(freq );
ph_hap1.push_back(h1 );
ph_hap2.push_back(h2 );
}
}
}
// Haploid possible phases
if (haploid || X )
{
for (int h1=0; h1<nh; h1++)
{
double freq = f[h1];
if (freq >= par::hap_min_phase_prob )
{
haploid_ph_freq.push_back(freq );
haploid_ph_hap1.push_back(h1 );
}
}
}
// Original total number of phases
np = ph_hap1.size();
haploid_np = haploid_ph_hap1.size();
}
// Legacy function: now redundant
/////////////////////////////////////////////
//////////////////////////////////////////////////
// Return a list of all possible haplotype names
vector<string> HaploPhase::returnHaplotypes(vector<int> & slist)
{
vector<string> str;
enumerateHaplotypes(slist );
for (int h=0; h<hap.size(); h++)
{
string hstr;
for (int s=0; s<ns; s++)
if (!hap[h][s])
hstr += P.locus[S[s]]->allele1;
else if (P.locus[S[s]]->allele2=="")
hstr += "0";
else
hstr += P.locus[S[s]]->allele2;
str.push_back(hstr);
}
return str;
}
//////////////////////////////////////////////////
// For multi-marker imputation and certain tasks,
// we require a 'test' haplotype
void HaploPhase::setTestHaplotype(string t)
{
// No specified test haplotype?
if ( t == "" )
{
test_hap = -1;
return;
}
// Create match template
vector<bool> tmp(ns, false);
for (int s=0; s<ns; s++)
if (P.locus[S[s]]->allele1 == t.substr(s, 1) )
tmp[s] = true;
// Consider each haplotype
test_hap = -1;
for (int h=0; h<hap.size(); h++)
{
bool match = true;
for (int s=0; s<ns; s++)
{
if (hap[h][s] != tmp[s])
{
match = false;
break;
}
}
if (match)
{
test_hap = h;
break;
}
}
}
void HaploPhase::reportHaplotypeFrequencies()
{
for (int h=0; h<nh; h++)
{
if (f[h] >= par::min_hf)
{
HFRQ << setw(10) << hname << " "<< setw(12) << haplotypeName(h)
<< " "<< setw(10) << f[h]<< "\n";
}
}
}
void HaploPhase::reportPhase()
{
string fn = par::output_file_name+".phase-"+hname;
ofstream PHASE(fn.c_str(), ios::out);
P.printLOG("Writing phased haplotypes for "+ hname + " to [ "+ fn + " ]\n");
PHASE << setw(par::pp_maxfid) << "FID" << " "
<< setw(par::pp_maxiid) << "IID"<< " "
<< setw(4) << "PH"<< " "
<< setw(10) << "HAP1"<< " "
<< setw(10) << "HAP2"<< " "
<< setw(12) << "POSTPROB"<< " "
// << setw(12) << "WEIGHT" << " "
<< setw(6) << "BEST"<< " "<< "\n";
PHASE.precision(4);
for (int i = 0; i < P.n; i++)
{
if (include[i])
{
for (int z = 0; z < hap1[i].size(); z++)
{
PHASE << setw(par::pp_maxfid) << P.sample[i]->fid<< " "
<< setw(par::pp_maxiid) << P.sample[i]->iid<< " "
<< setw(4) << z << " "
<< setw(10) << haplotypeName(hap1[i][z]) << " ";
if (haploid || (X && P.sample[i]->sex))
PHASE << setw(10) << haplotypeName( -1 ) << " ";
else
PHASE << setw(10) << haplotypeName(hap2[i][z]) << " ";
if (ambig[i])
{
PHASE << setw(12) << pp[i][z]<< " ";
int max_z = 0;
for (int z2=0; z2<hap1[i].size(); z2++)
max_z = pp[i][z2] > pp[i][max_z] ? z2 : max_z ;
if (max_z == z)
PHASE << setw(6) << 1<< " "<< " ";
else
PHASE << setw(6) << 0<< " "<< " ";
}
else
PHASE << setw(12) << 1<< " "<< setw(6) << 1<< " "<< " ";
// Genotypes
//for (int s=0; s<ns; s++)
//PHASE << genotype(P, i, S[s]) << " ";
PHASE << "\n";
}
}
// Report also on excluded individuals
// (Should be 0-size phase-set)
else
{
PHASE << setw(par::pp_maxfid) << P.sample[i]->fid << " "
<< setw(par::pp_maxiid) << P.sample[i]->iid << " "
<< setw(4) << "NA" << " "
<< setw(10) << "NA" << " "
<< setw(10) << "NA" << " "
<< setw(12) << "NA" << " "
<< setw(6) << "NA"<< " ";
// genotypes
// for (int s=0; s<ns; s++)
// PHASE << genotype(P, i, S[s]) << " ";
PHASE << "\n";
}
}
PHASE.close();
}
void HaploPhase::reportPhaseWideFormat()
{
string fn = par::output_file_name+".wphase-"+hname;
ofstream PHASE(fn.c_str(), ios::out);
P.printLOG("Writing wide-format phased haplotypes for "+ hname + " to [ "
+ fn + " ]\n");
PHASE << setw(par::pp_maxfid) << "FID"<< " "<< setw(par::pp_maxiid)
<< "IID"<< " ";
for (int h=0; h<nh; h++)
if (f[h] >= par::min_hf)
PHASE << setw(8) << "H_"+haplotypeName(h) << " ";
PHASE << "\n";
PHASE.precision(4);
for (int i = 0; i < P.n; i++)
{
if (include[i])
{
PHASE << setw(par::pp_maxfid) << P.sample[i]->fid<< " "
<< setw(par::pp_maxiid) << P.sample[i]->iid<< " ";
vector_t hcnt(nh, 0);
for (int z = 0; z < hap1[i].size(); z++)
{
if (ambig[i])
{
hcnt[hap1[i][z]] += pp[i][z];
if ( ! (haploid || (X && P.sample[i]->sex)))
hcnt[hap2[i][z]] += pp[i][z];
}
else
{
hcnt[hap1[i][z]] ++;
if ( ! (haploid || (X && P.sample[i]->sex)))
hcnt[hap2[i][z]] ++;
}
}
for (int h=0; h<nh; h++)
if (f[h] >= par::min_hf)
PHASE << setw(8) << hcnt[h]<< " ";
PHASE << "\n";
}
// Report also on excluded individuals
// (Should be 0-size phase-set)
else
{
PHASE << setw(par::pp_maxfid) << P.sample[i]->fid<< " "
<< setw(par::pp_maxiid) << P.sample[i]->iid<< " ";
for (int h=0; h<nh; h++)
if (f[h] >= par::min_hf)
PHASE << setw(8) << "NA"<< " ";
PHASE << "\n";
}
}
PHASE.close();
}
map<int,int> HaploPhase::makeSubHaplotypeSet(boolvec_t & mask)
{
map<int,int> t;
map<boolvec_t,int> shap;
int cnt=0;
for (int h=0; h < nh; h++)
{
boolvec_t sh;
for (int s = 0; s < ns ; s++)
{
if (mask[s])
sh.push_back(hap[h][s]);
}
map<boolvec_t,int>::iterator si = shap.find(sh);
if ( si == shap.end() )
{
shap.insert(make_pair(sh,cnt));
t.insert(make_pair(h,cnt));
++cnt;
}
else
t.insert(make_pair(h, si->second));
}
return t;
}
map<int,int> HaploPhase::makeTestSet(boolvec_t & mask, boolvec_t & allele)
{
map<int,int> tests;
for (int h2=0; h2 < nh; h2++)
{
bool is_A = true;
for (int s = 0; s < ns ; s++)
{
if (mask[s] && hap[h2][s] != allele[s])
is_A = false;
}
if (is_A )
tests.insert(make_pair(h2, 0));
else
tests.insert(make_pair(h2, 1));
}
return tests;
}
string HaploPhase::getSubHaplotypeName(boolvec_t & mask, boolvec_t & allele,
int blank)
{
string str = "";
for (int s=0; s < ns; s++)
{
if (s == blank )
str += " ";
else if (mask[s])
{
if (allele[s])
str += P.locus[ S[s] ]->allele1;
else
str += P.locus[ S[s] ]->allele2;
}
else
str += ".";
}
return str;
}
vector_t HaploPhase::imputeGenotype(int i, int l)
{
// Probability of AA, AB and BB for position 'l'
// (of ns SNPs) for individual 'i'
vector_t g(3);
if (X || haploid )
{
g[0] = g[1] = g[2] = 0;
return g;
error("HaploPhase::imputeGenotypess() not yet set up for X \n");
}
// Not able to be imputed?
if (!include[i])
{
g[0] = g[1] = g[2] = 0;
return g;
}
// Unambiguous imputation?
if (!ambig[i])
{
int h1 = hap1[i][0];
int h2 = hap2[i][0];
bool s1 = hap[h1][l];
bool s2 = hap[h2][l];
if (s1 != s2 )
g[1] = 1;
else if (s1 )
g[0] = 1;
else
g[2] = 1;
return g;
}
// Weighted, ambiguous imputation?
for (int z=0; z<hap1[i].size(); z++)
{
// ?? include?? if (pp[i][max_z] >= par::hap_post_prob)
int h1 = hap1[i][z];
int h2 = hap2[i][z];
bool s1 = hap[h1][l];
bool s2 = hap[h2][l];
if (s1 != s2 )
g[1] += pp[i][z];
else if (s1 )
g[0] += pp[i][z];
else
g[2] += pp[i][z];
} // next possible phase
return g;
}
double HaploPhase::imputeHaplotypes(int i, bool & n1, bool & n2)
{
// if ( X || haploid )
// error("HaploPhase::imputeHaplotypes() not yet set up for X \n");
bool actualX = X && P.sample[i]->sex;
//////////////////////////////////////////////
// Based on P(H|G) impute inferred haplotypes
// for above-threshold individuals
// Not imputed
double w = -1;
if ( ! include[i] )
{
n1 = true;
n2 = false;
return w;
}
// First for individuals of unambiguous phase
if (!ambig[i])
{
if (hap1[i][0] == test_hap)
n1 = false;
else
n1 = true;
if ( actualX || haploid )
{
n2 = n1;
}
else
{
if (hap2[i][0] == test_hap)
n2 = false;
else
n2 = true;
}
// Resolve potential het/missing coding confusion
if (n1 && (!n2))
{
n1 = false;
n2 = true;
}
// Unambiguous weighting (0, 1 or 2 copie of test_hap)
if (!n1)
{
if ( actualX || haploid )
w=1;
else
{
if (!n2)
w = 2;
else
w = 1;
}
}
else
w = 0;
}
else
{
// Second, for ambiguous individuals impute and assign weight
int max_z = 0;
for (int z=0; z<hap1[i].size(); z++)
max_z = pp[i][z] > pp[i][max_z] ? z : max_z ;
// Set missing by default
n1 = true;
n2 = false;
// Consider each phase z
// Above threshold?
if (pp[i][max_z] >= par::hap_post_prob)
{
// Do we match 'test_hap' ( '1' allele )
// or not? ( '2' allele )
if (hap1[i][max_z] == test_hap)
n1 = false;
else
n1 = true;
if ( actualX || haploid )
{
n2 = n1;
}
else
{
if (hap2[i][max_z] == test_hap)
n2 = false;
else
n2 = true;
}
// Resolve potential het/missing coding confusion
if (n1 && (!n2))
{
n1 = false;
n2 = true;
}
// Unambiguous weighting (1 or 2 copies of test_hap)
// We are saying either 0, 1 or 2 copies
// Consider each haplotype
// Number imputed / Actual number
for (int z=0; z<hap1[i].size(); z++)
{
if (hap1[i][z] == test_hap)
w += pp[i][z];
if ( ! ( actualX || haploid ))
{
if (hap2[i][z] == test_hap)
w += pp[i][z];
}
}
w = pp[i][max_z]/ w;
}
}
return w;
}
double HaploPhase::rsq_internal(int s1, int s2)
{
// A convenience function for SNP x SNP r^2
// i.e. here it does not matter which allele
// we consider, so just re-use mask
if (s1 > ns || s2 > ns )
error("Problem in rsq_internal(int,int)");
boolvec_t m1(ns, false);
boolvec_t m2(ns, false);
m1[s1] = true;
m2[s2] = true;
return rsq_internal(m1, m1, m2, m2);
}
double HaploPhase::rsq_internal(boolvec_t & mask1, boolvec_t & alleles1,
boolvec_t & mask2, boolvec_t & alleles2)
{
// Assume f[] has been populated with sensible values
// and hap[][] contains alleles
if (mask1.size() != ns ||mask2.size() != ns ||alleles1.size() != ns
||alleles2.size() != ns )
{
cout << ns << " "
<< mask1.size() << " "
<< mask2.size() << " "
<< alleles1.size() << " "
<< alleles2.size() << "\n";
error("Internal error in Phase::rsq");
}
// ---X-X- mask1
// 0-0 alleles1
// ----X-- mask2
// 1 alleles2
// i.e. find r^2 between 00 haplotype made of SNPs 4 & 6
// from 7 SNP haplotype with allele 1 of SNP 5
// Calculate frequency of first haplotype (fA)
double fA = 0;
double fB = 0;
double fAB = 0, fAb = 0, faB = 0, fab = 0;
for (int h = 0; h < nh; h++)
{
bool is_A = true;
bool is_B = true;
bool is_AB = true;
bool is_Ab = true;
bool is_aB = true;
for (int s = 0; s < ns ; s++)
{
if (mask1[s] && hap[h][s] != alleles1[s])
is_A = false;
if (mask2[s] && hap[h][s] != alleles2[s])
is_B = false;
if ( (mask1[s] && hap[h][s] != alleles1[s])
|| (mask2[s] && hap[h][s] != alleles2[s]))
is_AB = false;
if ( (mask1[s] && hap[h][s] != alleles1[s])
|| (mask2[s] && hap[h][s] == alleles2[s]))
is_Ab = false;
if ( (mask1[s] && hap[h][s] == alleles1[s])
|| (mask2[s] && hap[h][s] != alleles2[s]))
is_aB = false;
}
if (is_A )
fA += f[h];
if (is_B )
fB += f[h];
if (is_AB )
fAB += f[h];
else if (is_aB )
faB += f[h];
else if (is_Ab )
fAb += f[h];
else
fab += f[h];
// Next haplotype
}
double fa = 1 - fA;
double fb = 1 - fB;
// Calculate either r-sq or D'
double D = fAB - fA * fB;
if ( calculateDp )
{
double dmax1 = D > 0 ? fA * fb : fA * fB;
double dmax2 = D > 0 ? fa * fB : fa * fb;
double dmax = dmax1 < dmax2 ? dmax1 : dmax2;
if ( dmax == 0 )
return -1;
return D / dmax;
}
else
{
double denom = fA * fa * fB * fb;
if (denom == 0)
return -1;
return (D*D) / denom;
}
}
double HaploPhase::freq(boolvec_t & mask1, boolvec_t & alleles1)
{
// Assume f[] has been populated with sensible values
// and hap[][] contains alleles
if (mask1.size() != ns ||alleles1.size() != ns )
{
cout << ns << " "
<< mask1.size() << " "
<< alleles1.size() << "\n";
error("Internal error in Phase::freq");
}
// ---X-X- mask1
// 0-0 alleles1
double fA = 0;
for (int h = 0; h < nh; h++)
{
bool is_A = true;
for (int s = 0; s < ns ; s++)
{
if (mask1[s] && hap[h][s] != alleles1[s])
is_A = false;
}
if (is_A )
fA += f[h];
// Next haplotype
}
return fA;
}
double HaploPhase::rsq(int l1, int l2)
{
reset();
new_pred_locus.resize(1);
new_map.resize(1);