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homozyg.cpp
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homozyg.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 <vector>
#include <map>
#include <iterator>
#include <cmath>
#include "plink.h"
#include "helper.h"
#include "options.h"
#include "perm.h"
#include "stats.h"
#include "cnv.h"
extern Plink * PP;
namespace std
{
template<>
class less<Segment*> {
public:
bool operator()(Segment const* s1, Segment const* s2)
{
if ( s1->start > s2->start ) return true;
else if ( s1->start < s2->start ) return false;
else if ( s1->finish > s2->finish ) return true;
else if ( s1->p1 < s2->p1 ) return true;
else if ( s1->p1 > s2->p1 ) return false;
else if ( s1->p2 < s2->p2 ) return true;
else if ( s1->p2 > s2->p2 ) return false;
else return false;
}
};
};
class Pool
{
public:
set<Segment*,less<Segment*> > segs;
vector<vector<int> > match;
vector<int> matchcount;
vector<int> group;
vector<bool> index;
int chr;
int ng;
int min;
int max;
int union_min;
int union_max;
};
namespace std
{
template<>
class less<Pool*> {
public:
bool operator()(Pool const* p1, Pool const* p2)
{
if ( p1->segs.size() > p2->segs.size() ) return true;
else if ( p1->segs.size() < p2->segs.size() ) return false;
else
{
set<Segment*>::iterator s1 = p1->segs.begin();
set<Segment*>::iterator s2 = p2->segs.begin();
while ( s1 != p1->segs.end() )
{
if ( (*s1)->start > (*s2)->start ) return true;
else if ( (*s1)->start < (*s2)->start ) return false;
else if ( (*s1)->finish > (*s2)->finish ) return true;
else if ( (*s1)->finish < (*s2)->finish ) return false;
s1++;
s2++;
}
}
return false;
}
};
};
vector_t compareCNVs(CNVIndivReport & a,
CNVIndivReport & b)
{
vector_t res(8);
// t1 = # events in cases
// t2 = proportion of sample with 1+ event
// t6 = proportion of sample with at least gene
// t7 =
if ( par::segment_test_1sided )
{
res[0] = a.t1 - b.t1; // RATE
res[1] = a.t2 - b.t2; // PROP
res[2] = a.t3 - b.t3; // KBTOT
res[3] = a.t4 - b.t4; // KBAVG
res[4] = a.t5 - b.t5; // GRATE
res[5] = a.t6 - b.t6; // GPROP
res[6] = a.t7 - b.t7; // GRICH
res[7] = a.t8 - b.t8; // GRICH2
}
else
{
res[0] = fabs( a.t1 - b.t1 );
res[1] = fabs( a.t2 - b.t2 );
res[2] = fabs( a.t3 - b.t3 );
res[3] = fabs( a.t4 - b.t4 );
res[4] = fabs( a.t5 - b.t5 );
res[5] = fabs( a.t6 - b.t6 );
res[6] = fabs( a.t7 - b.t7 );
res[7] = fabs( a.t8 - b.t8 );
}
// cout << "DETS: "
// << a.count << " " << b.count << " -- G= "
// << a.t5 << " " << b.t5 << " -- B= "
// << a.t8 << " " << b.t8 << " -- EG= "
// << a.t9 << " " << b.t9 << " EB= "
// << a.t10 << " " << a.t10 << "\n";
return res;
}
// Helper function
void summaryIndivSummaries(Plink * P,
int kmask,
map<indivPair,int> & segmentCount,
map<indivPair,double> & segmentLength,
CNVIndivReport & a,
CNVIndivReport & u,
vector_t & res)
{
// Optionally only select individuals with kmask value,
// unless kmask < 0
// Return 2 (case/control) x object with
//
for ( int i = 0; i < P->n; i++)
{
Individual * person = P->sample[i];
if ( kmask >= 0 )
{
if ( person->sol != kmask )
continue;
}
indivPair t;
t.p1 = t.p2 = P->sample[i];
map<indivPair,int>::iterator ic = P->segmentCount.find(t);
map<indivPair,double>::iterator il = P->segmentLength.find(t);
map<indivPair,double>::iterator ic2 = P->segmentCount2.find(t);
map<indivPair,double>::iterator ic2b;
if ( par::cnv_count_baseline )
ic2b = P->segmentCount2Baseline.find(t);
//indivPair p = ic->first;
if ( person->pperson->aff )
++a.n;
else
++u.n;
if ( ic == P->segmentCount.end() )
continue;
CNVIndivReport * pstat = person->pperson->aff ? &a : &u;
// Basic CNV properties
pstat->t1 += ic->second;
pstat->t2++;
pstat->t3 += il->second;
pstat->t4 += il->second / (double)ic->second;
// Geneset count statistics
pstat->t5 += ic2->second;
pstat->t6 += ic2->second > 0 ? 1 : 0;
pstat->t7 += (double)ic2->second / (double)il->second;
pstat->t9 += PP->expectedOverlap[i];
// cout << " overlap = " << ic2->second << " of " << PP->expectedOverlap[i] << "\n";
// Baseline/comparator geneset counts
if ( par::cnv_count_baseline )
{
if ( ic2b->second>0) pstat->count_baseline++;
pstat->t8 += ic2b->second;
pstat->t10 += PP->expectedOverlapBaseline[i];
// cout << "bline = " << ic2b->second << " " << PP->expectedOverlapBaseline[i] << "\n";
}
pstat->count++;
} // Next individual
// edit to make denom of t8 test total # of individuals
// a.count_baseline = a.count;
// u.count_baseline = u.count;
// Save actual segment counts before we make the means
a.segCount = (int)a.t1;
u.segCount = (int)u.t1;
////////////////////////////////////////
// Get means
a.calculateResults();
u.calculateResults();
res = compareCNVs(a,u);
}
/////////////////////////////////////////////
// Entrypoint for all homozygosity run tests
void Plink::findAllHomozygousRuns(Perm & perm)
{
if (par::SNP_major) SNP2Ind();
string f = par::output_file_name + ".hom";
// Calculate or read homozygous segments from a file?
if ( ! par::read_segment_file )
{
ofstream HOM;
HOM.open(f.c_str(),ios::out);
HOM.precision(3);
HOM.setf(ios::fixed);
printLOG("\nWriting homozygosity-run information to [ "+f+" ] \n");
printLOG("Run defined as: ");
if (par::homo_run_kb)
{
printLOG(int2str(par::homo_run_length_kb)+" kb ");
if (par::homo_run_snps) printLOG(", ");
}
if (par::homo_run_snps)
printLOG(int2str(par::homo_run_length_snps)+" SNPs");
printLOG("\n");
// printLOG("Allowing "+int2str(par::homo_run_het)+" hets per run\n");
HOM << setw(par::pp_maxfid) << "FID" << " "
<< setw(par::pp_maxiid) << "IID" << " "
<< setw(8) << "PHE" << " "
<< setw(4) << "CHR" << " "
<< setw(par::pp_maxsnp) << "SNP1" << " "
<< setw(par::pp_maxsnp) << "SNP2" << " "
<< setw(12) << "POS1" << " "
<< setw(12) << "POS2" << " "
<< setw(10) << "KB" << " "
<< setw(8) << "NSNP" << " "
<< setw(8) << "DENSITY" << " "
<< setw(8) << "PHOM" << " "
<< setw(8) << "PHET" << "\n";
printLOG("Homozygous segment criteria:\n");
printLOG(" length (kb) = " + int2str(par::homo_run_length_kb) + "\n");
printLOG(" # SNPs (N) = " + int2str(par::homo_run_length_snps) + "\n");
printLOG(" density (kb/SNP) = " + dbl2str(par::homo_run_density) + "\n");
printLOG(" largest gap (kb) = " + int2str(par::homo_run_gap) + "\n");
// Rescale GAP to base-pairs
par::homo_run_gap *= 1000;
// Find segments for each individual
for (int i1=0; i1<n; i1++)
{
if (!par::silent)
cout << i1+1 << " of " << n << " individuals \r";
// findHomoRuns(sample[i1], HOM);
findHomoWindow(sample[i1], HOM);
}
if (!par::silent)
cout << "\n\n";
HOM.close();
}
else
{
// Read segments from a file
ifstream SEG;
SEG.open(par::read_segment_filename.c_str(),ios::in);
printLOG("Reading homozygous-segment information from [ "
+par::read_segment_filename+" ]\n");
checkFileExists(par::read_segment_filename);
readHomozygSegmentFile(SEG);
SEG.close();
}
///////////////////////////////////
// Display summary by individual
printLOG("Writing segment summary to [ " + f +".indiv ]\n");
indivSegmentSummary();
///////////////////////////////////
// Display summary (i.e. per locus)
printLOG("Writing segment summary to [ " + f +".summary ]\n\n");
summaryIBSsegments(perm);
//////////////////////////////////////
// Look for shared homozygous regions
// if --homo-match option given
if (par::homo_summary_allelic_match)
summariseHomoRuns();
}
// Homozygosity match, whole segments
bool segsMatch(Segment * s1, Segment * s2)
{
if ( par::cnv_list )
return true;
int mismatch = 0;
int start = s1->start > s2->start ? s1->start : s2->start;
int finish = s1->finish < s2->finish ? s1->finish : s2->finish;
// Assume individual major mode
for (int l=start; l<= finish; l++)
{
// Only test homozygotes
if ( s1->p1->one[l] == s1->p1->two[l] &&
s2->p1->one[l] == s2->p1->two[l] )
if ( s1->p1->one[l] != s2->p1->one[l] )
mismatch++;
}
if ((double)mismatch/(double)(finish-start+1) > 1-par::fuzzy_homo ) return false;
else return true;
}
// Homozygosity Match, supplying pool consensus start/finish
bool segsIBDMatchCON(Segment * s1, Segment * s2, int start, int finish)
{
int match = 0;
int valid = 0;
// 1. Determine which allele is shared for each pair
// 2. See whether this is the same allele between pairs
// Assume individual major mode
for (int l=start; l<= finish; l++)
{
// Ignore is 1+ missing or 2 hets
bool a1 = s1->p1->one[l];
bool a2 = s1->p1->two[l];
bool b1 = s1->p2->one[l];
bool b2 = s1->p2->two[l];
bool c1 = s2->p1->one[l];
bool c2 = s2->p1->two[l];
bool d1 = s2->p2->one[l];
bool d2 = s2->p2->two[l];
bool allele1 = false;
bool allele2 = false;
// Any missing alleles?
if ( (a1 && (!a2)) ||
(b1 && (!b2)) ||
(c1 && (!c2)) ||
(d1 && (!d2)) )
continue;
// Any double hets within each pair?
if ( ((!a1) && a2) &&
((!b1) && b2) )
continue;
if ( (!c1) && c2 &&
(!d1) && d2 )
continue;
// Any opposing homozygotes within pair?
if ( (a1 == a2) &&
(b1 == b2) &&
(a1 != b1) )
continue;
if ( (c1 == c2) &&
(d1 == d2) &&
(c1 != d1) )
continue;
// Get the alleles for the pairs
// (i.e. from the homozygote)
if ( a1 == a2 ) allele1 = a1;
else allele1 = b1;
if ( c1 == c2 ) allele2 = c1;
else allele2 = d1;
// Do these match?
if ( allele1 == allele2 )
match++;
valid++;
}
if ( valid<par::genome_test_min_snp ) return false;
if ((double)match/(double)valid < par::fuzzy_homo ) return false;
else return true;
}
// Pairwise segmental match, whole segments
bool segsIBDMatch(Segment * s1, Segment * s2)
{
int match = 0;
int valid = 0;
int start = s1->start > s2->start ? s1->start : s2->start;
int finish = s1->finish < s2->finish ? s1->finish : s2->finish;
// 1. Determine which allele is shared for each pair
// 2. See whether this is the same allele between pairs
// Assume individual major mode
for (int l=start; l<= finish; l++)
{
// Ignore is 1+ missing or 2 hets
bool a1 = s1->p1->one[l];
bool a2 = s1->p1->two[l];
bool b1 = s1->p2->one[l];
bool b2 = s1->p2->two[l];
bool c1 = s2->p1->one[l];
bool c2 = s2->p1->two[l];
bool d1 = s2->p2->one[l];
bool d2 = s2->p2->two[l];
bool allele1 = false;
bool allele2 = false;
// Any missing alleles?
if ( (a1 && (!a2)) ||
(b1 && (!b2)) ||
(c1 && (!c2)) ||
(d1 && (!d2)) )
continue;
// Any double hets within each pair?
if ( ((!a1) && a2) &&
((!b1) && b2) )
continue;
if ( (!c1) && c2 &&
(!d1) && d2 )
continue;
// Any opposing homozygotes within pair?
if ( (a1 == a2) &&
(b1 == b2) &&
(a1 != b1) )
continue;
if ( (c1 == c2) &&
(d1 == d2) &&
(c1 != d1) )
continue;
// Get the alleles for the pairs
// (i.e. from the homozygote)
if ( a1 == a2 ) allele1 = a1;
else allele1 = b1;
if ( c1 == c2 ) allele2 = c1;
else allele2 = d1;
// Do these match?
if ( allele1 == allele2 )
match++;
valid++;
}
if ( valid<par::genome_test_min_snp ) return false;
if ((double)match/(double)valid < par::fuzzy_homo ) return false;
else return true;
}
// Pairwise segmental match, supplying pool consensus start/finish
bool segsMatchCON(Segment * s1, Segment * s2, int start, int finish)
{
if ( par::cnv_list )
return true;
int mismatch = 0;
// Assume individual major mode
for (int l=start; l<= finish; l++)
{
// Only test homozygotes
if ( s1->p1->one[l] == s1->p1->two[l] &&
s2->p1->one[l] == s2->p1->two[l] )
if ( s1->p1->one[l] != s2->p1->one[l] )
mismatch++;
}
if ((double)mismatch/(double)(finish-start+1) > 1-par::fuzzy_homo ) return false;
else return true;
}
void displayPoolVerbose( Plink & P, Pool * pool , ofstream & OUT )
{
// Figure out list of individuals, for the maximal region
// i.e. union rather than intersection of the pool of segs
set<Individual*> pset;
vector<set<Individual*> > pgrpset( pool->ng );
vector<Individual*> plist;
vector<int> pstart;
vector<int> pend;
vector<int> pgrp;
// Loop over each group in the pool
for ( int g = 0; g < pool->ng; g++)
{
// Consider all segments in this pool
set<Segment*>::iterator s = pool->segs.begin();
int c2=0;
while ( s != pool->segs.end() )
{
// Not in group 'g' ?
if ( pool->group[c2] == g )
{
if ( pset.find( (*s)->p1 ) == pset.end() )
{
pset.insert( (*s)->p1 );
plist.push_back( (*s)->p1 );
pstart.push_back( (*s)->start );
pend.push_back( (*s)->finish );
pgrp.push_back( g );
}
if ( pset.find( (*s)->p2 ) == pset.end() )
{
pset.insert( (*s)->p2 );
plist.push_back( (*s)->p2 );
pstart.push_back( (*s)->start );
pend.push_back( (*s)->finish );
pgrp.push_back( g );
}
// Add to group-specfic unique individual list
if ( pgrpset[g].find( (*s)->p1 ) == pgrpset[g].end() )
{
pgrpset[g].insert( (*s)->p1 );
}
if ( pgrpset[g].find( (*s)->p2 ) == pgrpset[g].end() )
{
pgrpset[g].insert( (*s)->p2 );
}
}
// Next segment
s++;
c2++;
continue;
}
}
// We now a have a unique list of individuals, in the same order in plist as
// the grouping variable; now display, each row is a SNP
// Header row (including IDs)
OUT << setw(6) << " " << " "
<< setw(par::pp_maxfid) << "FID" << " "
<< setw(par::pp_maxiid) << "IID" << " "
<< setw(4) << "GRP" << " "
<< "\n";
for (int i=0; i < plist.size(); i++)
{
OUT << setw(6) << int2str(i+1)+") " << " "
<< setw(par::pp_maxfid) << plist[i]->fid << " "
<< setw(par::pp_maxiid) << plist[i]->iid << " ";
// Display the group(s) this individual belongs to
bool any = false;
for ( int g = 1 ; g < pool->ng; g++ )
{
if ( pgrpset[g].find(plist[i]) != pgrpset[g].end() )
{
if (!any) any = true;
else OUT << ", ";
OUT << g;
}
}
OUT << "\n";
}
OUT << "\n" << setw(par::pp_maxsnp) << "SNP" << " ";
for (int i=0; i < plist.size(); i++)
OUT << setw(5) << int2str(i+1)+" " << " ";
OUT << "\n\n";
///////////////////////////////////////////////////////
// Forcing a single pool? In this case, only display
// the selected region, rather than the whole thing
// (note: we have already displayed the union in the
// *.overlap file, so okay to change this now
if ( par::force_span )
{
pool->union_min = par::segment_snp1;
pool->union_max = par::segment_snp2;
}
///////////////////////////////////////////////////////
// Display all SNPs
for (int l = pool->union_min ; l <= pool->union_max ; l++)
{
if (! par::force_span ) if ( l == pool->min ) OUT << "\n";
OUT << setw(par::pp_maxsnp) << P.locus[l]->name << " ";
// Consider all individuals (in plist)
for (int i=0; i < plist.size(); i++)
{
if ( l >= pstart[i] && l <= pend[i] )
OUT << setw(5) << "["+genotype(P,plist[i],l)+"]" << " ";
else
OUT << setw(5) << " "+genotype(P,plist[i],l)+" " << " ";
}
OUT << "\n";
if (! par::force_span ) if ( l == pool->max ) OUT << "\n";
}
OUT << "\n\n";
///////////////////////////////////////////////////////
// Finally, find the consensus haplotype for each group
// For example, pair within a group, for their overlap only
// count number of greatest allele of the 4
// Exactly the same principle applies whether looking at homozygous
// or heterozygous runs; this will implicitly ignore double hets;
// and provide a sensible way of dealing with missing data, hets in
// homozygous runs, etc
vector<string> ghap(pool->ng,"");
for ( int g = 1; g < pool->ng; g++)
{
OUT << "Group " << g << "\n\n";
for (int i=0; i < plist.size(); i++)
{
// Is this individual in this group?
if ( pgrpset[g].find(plist[i]) != pgrpset[g].end() )
{
Individual * person = plist[i];
OUT << setw(6) << int2str(i+1)+") "
<< setw(par::pp_maxfid) << person->fid << " "
<< setw(par::pp_maxiid) << person->fid << " "
<< setw(8) << person->phenotype << "\n";
}
}
OUT << "\n";
OUT << "\n" << setw(par::pp_maxsnp) << "SNP" << " "
<< setw(6) << " " << " ";
for (int i=0; i < plist.size(); i++)
if ( pgrpset[g].find(plist[i]) != pgrpset[g].end() )
OUT << setw(5) << int2str(i+1)+" " << " ";
OUT << "\n\n";
// Consider each position
for (int l = pool->union_min ; l <= pool->union_max ; l++)
{
if (! par::force_span ) if ( l == pool->min ) OUT << "\n";
OUT << setw(par::pp_maxsnp) << P.locus[l]->name << " ";
// Loop over each group in the pool (start from 1..ng)
// (0 is unassigned)
// Keep track of most likely allele for this position for this group
int a1count = 0 ;
int a2count = 0 ;
// Consider all segments in this pool
set<Segment*>::iterator s = pool->segs.begin();
int c2=0;
while ( s != pool->segs.end() )
{
// Only count of this segment is spanning this particular
// position
if ( l >= (*s)->start && l <= (*s)->finish )
{
// Not in group 'g' ?
if ( pool->group[c2] == g )
{
// Consider genotypes of p1, p2: get count of 4 alleles
bool a1 = (*s)->p1->one[l];
bool a2 = (*s)->p1->two[l];
bool b1 = (*s)->p2->one[l];
bool b2 = (*s)->p2->two[l];
// Homozygote?
if ( a1 == a2 )
{
if ( a1 )
a2count++;
else
a1count++;
}
if ( b1 == b2 )
{
if ( b1 )
a2count++;
else
a1count++;
}
}
}
// Next segment
s++;
c2++;
continue;
} // Next segment in group
///////////////////////////////////////////
// Display this group's consensus haplotype
string str = "?";
if ( a1count > a2count )
str = P.locus[l]->allele1;
else if ( a2count > a1count )
str = P.locus[l]->allele2;
OUT << setw(2) << str << " "
<< setw(4) << " " << " ";
ghap[g] += str;
///////////////////////////////////////////
// Consider all individuals (in plist)
for (int i=0; i < plist.size(); i++)
{
if ( pgrpset[g].find(plist[i]) != pgrpset[g].end() )
//if ( pgrp[i] == g )
{
if ( l >= pstart[i] && l <= pend[i] )
OUT << setw(5) << "["+genotype(P,plist[i],l)+"]" << " ";
else
OUT << setw(5) << " "+genotype(P,plist[i],l)+" " << " ";
}
}
OUT << "\n";
if (! par::force_span ) if ( l == pool->max ) OUT << "\n";
} // Next SNP
OUT << "\n";
} // Next group
OUT << "\n\n";
// Consider each position
int lp=0;
for (int l = pool->union_min ; l <= pool->union_max ; l++)
{
if (! par::force_span ) if ( l == pool->min ) OUT << "\n";
OUT << setw(par::pp_maxsnp) << P.locus[l]->name << " ";
for ( int g = 1; g < pool->ng; g++)
{
OUT << ghap[g][lp] << " ";
}
lp++;
OUT << "\n";
if (! par::force_span ) if ( l == pool->max ) OUT << "\n";
}
}
void Plink::groupSegmentsSpanning(int l)
{
// Find list of segments spanning SNP 'l'
// and return as a vector of ints -- this
// is just a convenience wrapper around
// summariseHomoRuns()
par::force_span = true;
par::segment_current_focal_snp = l;
par::segment_silently_return_groups = true;
bool old_silent = par::silent;
par::silent = true;
// A value of -1 means no segment
indivSegmentGroup.resize(n);
for (int i=0; i<n; i++)
indivSegmentGroup[i] = -1;
// This currently only works for homozygosity (i.e. where each
// individual can only belong to one group)
// Populate Plink::indivSegmentGroup[]
summariseHomoRuns();
par::silent = old_silent;
}
void Plink::summariseHomoRuns()
{
ofstream HOM;
////////////////////////////////
// Output to screen, files, etc
if ( ! par::segment_silently_return_groups )
{
if ( par::cnv_list )
{
par::segment_overlap = false;
par::fuzzy_homo = 0;
}
// Codes:
// CNVs -- par::cnv_list
// IBD -- par::segment_overlap
// HBD -- par::homo_run
string f;
if ( par::cnv_list )
f = par::output_file_name + ".cnv.overlap";
else if (par::segment_overlap)
f = par::output_file_name + ".segment.overlap";
else
f = par::output_file_name + ".hom.overlap";
HOM.open(f.c_str(),ios::out);
HOM.precision(6);
if ( par::cnv_list )
printLOG("Writing CNV summary to [ "+f+" ] \n");
else if (par::segment_overlap)
printLOG("Writing IBD-run summary to [ "+f+" ] \n");
else
printLOG("Writing homozygosity-run summary to [ "+f+" ] \n");
if (par::segment_verbose)
printLOG("Writing IBD-run summary to [ "
+ par::output_file_name
+ ".segment.overlap.*.verbose"+" ] \n");
else if (par::homozyg_verbose)
printLOG("Writing homozygosity-run summary to [ "
+ par::output_file_name
+ ".hom.overlap.*.verbose"+" ] \n");
if ( ! par::cnv_list)
{
if (par::fuzzy_homo > 1e-6)
{
printLOG("Requiring allelic match, threshold "
+ dbl2str(par::fuzzy_homo)+" identity\n");
printLOG("Requiring at least "
+ int2str(par::genome_test_min_snp)
+ " informative SNPs to match segments\n");