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gvar.cpp
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//////////////////////////////////////////////////////////////////
// //
// PLINK (c) 2005-2008 Shaun Purcell //
// //
// This file is distributed under the GNU General Public //
// License, Version 2. Please see the file COPYING for more //
// details //
// //
//////////////////////////////////////////////////////////////////
#include "gvar.h"
#include "helper.h"
#include "options.h"
#include "plink.h"
#include "model.h"
#include "logistic.h"
#include "linear.h"
#include "stats.h"
#include <iostream>
#include <iomanip>
#include <fstream>
#include <sstream>
#include <limits>
#include <errno.h>
// A couple of helper functions
Model * analyseModel(Plink *, Variant *, int, bool, bool);
double compareModels(Model *, Model *) ;
class fullGenotype{
public:
fullGenotype(int2 a, int2 b)
{
a1 = a;
a2 = b;
if ( a1 < a2 )
{
int2 t = a1;
a1 = a2;
a2 = t;
}
}
int2 a1;
int2 a2;
bool operator< (const fullGenotype & b) const
{
return (a1 < b.a1 || (a1 == b.a1 && a2 < b.a2) );
}
};
void Plink::readGenericVariantData()
{
///////////////////////////////////////////////
// Load data (if par::gvar is true) -- otherwise,
// we are just
string filename = par::gvarfile;
if ( par::gvar )
checkFileExists( filename );
// If we are not reading in any generic variants,
// but we have elected to write a file, then
// we must set this flag so that the data are
// carried over
if ( par::gvar_write && ! par::gvar )
par::gvar_include_all_variants = true;
///////////////////////////////////////////////
// Input mode
//
// 1) Either we start from scratch, read in gMAP file
// and then data (par::load_gvar is true)
// 2) Or, we have first read in the standard file, and we
// just place these on top, copying basic SNPs over first
// (par::load_gvar is false)
bool preexisting = locus.size() > 0;
// We need either basic SNPs or generic variants here
if ( ! ( preexisting || par::gvar ) )
return;
if ( preexisting )
{
nl_all = locus.size();
n = sample.size();
// prettyPrintLengths();
}
///////////////////////////////////////////////
// .map file
vector<bool> include;
vector<int> include_pos(0);
if ( par::gvar && !preexisting )
{
checkFileExists( par::gmapfile );
ngvar = 0;
readMapFile(par::gmapfile,
include,
include_pos,
ngvar);
gvar.clear();
for (int l=0; l<locus.size(); l++)
{
gvar.push_back( (Variant *)(locus[l]) );
gvar[l]->acode.clear();
}
locus.clear();
}
///////////////////////////////////////////////
// Otherwise figure out which markers to keep
// i.e. assume a small subset of all
set<string> observedGVARs;
map<int,int> copyover;
if ( preexisting )
{
// Either take all SNPs in memory, or
// select out just those already specified in
// the GVAR file
if ( par::gvar_include_all_variants )
{
// Copy all SNPs over
for (int l=0; l<nl_all; l++)
observedGVARs.insert( locus[l]->name );
ngvar = observedGVARs.size();
}
else if ( par::gvar )
{
FILE * GV;
GV = fopen64( filename.c_str(),"r");
if ( GV == NULL )
error("Problem opening GVAR file, errno = "+int2str(errno));
while ( ! feof(GV) )
{
string dummy;
string gvarname;
int f=0;
if ( readString( GV , dummy ) ) ++f;
if ( dummy == "" )
continue;
if ( readString( GV , dummy ) ) ++f;
if ( readString( GV , gvarname ) )
observedGVARs.insert( gvarname );
while (fgetc(GV) != '\n' && !feof(GV)) {}
}
fclose(GV);
ngvar = observedGVARs.size();
printLOG("Found "+int2str( ngvar )+" variant in [ " + filename + " ]\n");
}
//////////////////////////////////
// Copy MAP into appropriate space
gvar.clear();
map<string,int> im;
for (int l=0; l<locus.size(); l++)
im.insert(make_pair( locus[l]->name, l));
set<string>::iterator is = observedGVARs.begin();
while ( is != observedGVARs.end() )
{
map<string,int>::iterator imi = im.find( *is );
if ( imi != im.end() )
{
Variant * gloc = new Variant;
Locus * loc = locus[imi->second];
gloc->name = loc->name;
gloc->chr = loc->chr;
gloc->bp = loc->bp;
gloc->pos = loc->pos;
gloc->acode.clear();
gloc->alleles.clear();
gvar.push_back( gloc );
int l = gvar.size() - 1;
copyover.insert(make_pair(l,imi->second));
}
else
error("Generic variant "
+ *is
+ " found that was not in original SNP file\n");
++is;
}
}
///////////////////////////////////////////////
// .fam
if ( par::gvar && ! preexisting )
{
checkFileExists( par::gfamfile );
readFamFile(par::gfamfile);
n = sample.size();
// Read an alternate phenotype file?
if (par::pheno_file)
readPhenoFile();
if ( par::bt )
affCoding(*this);
}
///////////////////////////////////////////////
// Allocate space
for (int i=0; i<sample.size(); i++)
{
sample[i]->gvar.resize( ngvar );
for (int g=0; g<ngvar; g++)
sample[i]->gvar[g] = new GVariant;
}
///////////////////////////////////////////////
// Copy over any existing SNP data
if ( preexisting )
{
for (int g=0; g<ngvar; g++)
{
Variant * gloc = gvar[g];
map<int,int>::iterator li = copyover.find(g);
int l = li->second;
Locus * loc = locus[ li->second ];
int acode1 = -1;
int acode2 = -1;
if ( loc->allele1 != "" && loc->allele1 != par::missing_genotype )
{
if ( gloc->acode.find( loc->allele1 ) == gloc->acode.end() )
{
gloc->acode.insert( make_pair( loc->allele1, gloc->nallele ));
gloc->alleles.push_back( loc->allele1 );
acode1 = gloc->nallele;
++(gloc->nallele);
}
}
if ( loc->allele2 != "" && loc->allele2 != par::missing_genotype )
{
if ( gloc->acode.find( loc->allele2 ) == gloc->acode.end() )
{
gloc->acode.insert( make_pair( loc->allele2, gloc->nallele ));
gloc->alleles.push_back( loc->allele2 );
acode2 = gloc->nallele;
++(gloc->nallele);
}
}
// Now copy over actual genotypes for this particular SNP
// allele
for (int i=0; i<sample.size(); i++)
{
GVariant * gv = sample[i]->gvar[g];
gv->allele1 = gv->allele2 = -1;
bool s1 = par::SNP_major ? SNP[l]->one[i] : sample[i]->one[l];
bool s2 = par::SNP_major ? SNP[l]->two[i] : sample[i]->two[l];
// Missing genotype
if ( s1 && ! s2 )
{
gv->missing = true;
continue;
}
gv->missing = false;
if ( s1 )
{
gv->allele1 = gv->allele2 = acode2;
}
else
{
if ( s2 )
{
// if ( sample[i]->sex )
// cout << "het male??? " << sample[i]->fid << "\n";
gv->allele1 = acode1;
gv->allele2 = acode2;
}
else
{
gv->allele1 = acode1;
gv->allele2 = acode1;
}
}
/////////////////////////////////////////////
// Autosomal or haploid? Should have already
// blanked out hemizygous haploid calls
if ( par::chr_haploid[gloc->chr] ||
( par::chr_sex[gloc->chr] && sample[i]->sex ) )
{
gv->dosage1 = 1;
gv->dosage2 = 0;
}
else
{
gv->dosage1 = 1;
gv->dosage2 = 1;
}
}
}
}
///////////////////////////////////////////////
// .gvar
FILE * GV;
if ( par::gvar )
{
GV = fopen64( filename.c_str(),"r");
if ( GV == NULL )
error("Problem opening GVAR file, errno = "+int2str(errno));
// We can now read any number of individual/genotype lines, in any
// order; we also do not assume that all genotypes are given --
// these will be missing by default
map<string,int> imap;
if ( ! preexisting )
{
for (int i=0; i<include.size(); i++)
{
if ( include[i] )
{
int k = include_pos[i];
imap.insert( make_pair ( locus[k]->name , k ) );
}
}
}
else
{
include.clear();
include.resize( ngvar, true );
include_pos.clear();
for (int i=0; i<include.size(); i++)
{
include_pos.push_back(i);
imap.insert( make_pair ( gvar[i]->name , i ) );
}
}
map<string,int> iperson;
for (int i=0; i<sample.size(); i++)
{
iperson.insert( make_pair
( sample[i]->fid + "_" + sample[i]->iid ,
i ) );
}
// Whether or not we want to look at a locus is in the include[] vector
// The genomic position of locus i is k=include_pos[i] -> locus[k]
bool fatal = false;
string fmsg = "";
while( ! feof(GV) )
{
string fid = "";
string iid = "";
string gvarname = "";
string one = "";
string dose1 = "";
string two = "";
string dose2 = "";
int f = 0;
if ( readString( GV , fid ) ) f++;
if ( fid == "" )
continue;
if ( readString( GV , iid ) ) f++;
if ( readString( GV , gvarname ) ) f++;
if ( readString( GV , one ) ) f++;
if ( readString( GV , dose1 ) ) f++;
if ( readString( GV , two ) ) f++;
if ( readString( GV , dose2 ) ) f++;
map<string,int>::iterator peri
= iperson.find( fid+"_"+iid );
Individual * person =
peri != iperson.end() ?
sample[peri->second] : NULL ;
map<string,int>::iterator im = imap.find( gvarname );
int k =
im != imap.end() ?
im->second : -1;
// Ignore this genotype?
if ( ( ! person ) || k < 0 )
continue;
double d1, d2;
if ( ( ! from_string<double>( d1, dose1, std::dec) )
|| ( ! from_string<double>( d2, dose2, std::dec) ) )
error("Problem in format of file [ " + filename + " ]\n\n"
+fid+" "+iid+" "+gvarname+" "
+one+" "+dose1+" "
+two+" "+dose2+"\n");
int ip = peri->second;
Variant * gloc = gvar[k];
GVariant * g = person->gvar[k];
/////////////////////////////////////////
// Add allele names to list, if needed
if ( ( one == par::missing_genotype && d1 > 0 ) ||
( two == par::missing_genotype && d2 > 0 ) )
{
g->missing = true;
continue;
}
g->missing = false;
map<string,int>::iterator ia = gloc->acode.find( one );
if ( d1 > 0 )
{
if ( ia == gloc->acode.end() )
{
gloc->acode.insert( make_pair( one, gloc->nallele ));
gloc->alleles.push_back( one );
g->allele1 = gloc->nallele;
++(gloc->nallele);
}
else
g->allele1 = ia->second;
}
else
g->allele1 = -1;
// Store second allele
ia = gloc->acode.find( two );
if ( d2 > 0 )
{
if ( ia == gloc->acode.end() )
{
gloc->acode.insert( make_pair( two, gloc->nallele ));
gloc->alleles.push_back( two );
g->allele2 = gloc->nallele;
++(gloc->nallele);
}
else
g->allele2 = ia->second;
}
else
g->allele2 = -1;
// Store dosage information
g->dosage1 = d1;
g->dosage2 = d2;
// Have we seen any non-integer dosages?
if ( d1 - int(d1) > 1e-6 ||
d2 - int(d2 ) > 1e-6 )
gloc->integerDosage = false;
}
fclose(GV);
}
/////////////////////////////
// Clear up any old SNP data
if ( preexisting )
{
for (int l=0; l<locus.size(); l++)
delete locus[l];
if (par::SNP_major)
for (int l=0; l<SNP.size(); l++)
delete SNP[l];
else
for (int i=0; i<sample.size(); i++)
{
sample[i]->one.clear();
sample[i]->two.clear();
}
SNP.clear();
locus.clear();
}
}
void Plink::processGVAR()
{
// Use the Model class to test generic variants,
// but not entering any main SNP effects
par::assoc_glm_without_main_snp = true;
printLOG("Processing data for "
+ int2str( ngvar )
+ " generic variants\n");
ofstream GOUT;
ofstream GVERB;
if ( true )
{
printLOG("Writing frequency & genotyping informtion to [ "
+ par::output_file_name
+ ".gvar.summary ]\n");
GOUT.open( ( par::output_file_name
+ ".gvar.summary").c_str(), ios::out );
GOUT.precision(4);
GOUT << setw(16) << "NAME" << " "
<< setw(12) << "FIELD" << " "
<< setw(12) << "VALUE" << "\n";
}
if ( par::gvar_verbose_association )
{
GVERB.open((par::output_file_name+".assoc.gvar").c_str(),ios::out);
printLOG("Writing verbose GVAR association results to [ "
+ par::output_file_name + ".assoc.gvar ]\n");
}
/////////////////////////////////////
// Is there any phenotypic variation?
bool phenotypicVariation = false;
for (int i=1; i<n; i++)
{
if ( sample[i-1]->missing ) continue;
if ( sample[i]->missing ) continue;
if ( sample[i-1]->phenotype != sample[i]->phenotype )
{
phenotypicVariation = true;
break;
}
}
for (int g=0; g<ngvar; g++)
{
Variant * v = gvar[g];
GOUT << setw(16) << v->name << " "
<< setw(12) << "CHR" << " "
<< setw(12) << v->chr << "\n";
GOUT << setw(16) << v->name << " "
<< setw(12) << "BP" << " "
<< setw(12) << v->bp << "\n";
vector_t f( v->nallele );
map<int,int> cnvCount;
int sampleTotalDose = 0;
int sampleTotalInd = 0;
map<fullGenotype,int2> typeCount;
map<fullGenotype,int2>::iterator tit;
for (int i=0; i<n; i++)
{
Individual * person = sample[i];
if ( person->missing )
continue;
GVariant * gv = person->gvar[g];
if ( gv->missing )
{
int2 p(-1,1);
fullGenotype fg(p,p);
tit = typeCount.find(fg);
int2 q(0,0);
if ( person->aff )
q.p1=1;
else
q.p2=1;
if ( tit == typeCount.end() )
typeCount.insert(make_pair(fg,q));
else
{
if ( person->aff )
++(tit->second.p1);
else
++(tit->second.p2);
}
continue;
}
/////////////////////////
// Calculate frequencies
if ( gv->allele1 >= 0 )
f[ gv->allele1 ] += gv->dosage1;
if ( gv->allele2 >= 0 )
f[ gv->allele2 ] += gv->dosage2;
int totalDose = (int)(gv->dosage1 + gv->dosage2);
cnvCount[totalDose]++;
sampleTotalDose += totalDose;
// Keep track of specific allele/CNV counts
// by case/control status
if ( person->aff || par::qt )
{
int2 p(gv->allele1,(int)gv->dosage1);
int2 q(gv->allele2,(int)gv->dosage2);
fullGenotype fg(p,q);
tit = typeCount.find(fg);
if ( tit == typeCount.end() )
typeCount.insert(make_pair(fg,int2(1,0)));
else
++(tit->second.p1);
}
else
{
int2 p(gv->allele1,(int)gv->dosage1);
int2 q(gv->allele2,(int)gv->dosage2);
fullGenotype fg(p,q);
tit = typeCount.find(fg);
if ( tit == typeCount.end() )
typeCount.insert(make_pair(fg,int2(0,1)));
else
++(tit->second.p2);
}
++sampleTotalInd;
} // Look at next individual
v->allelicVariation = false;
int commonAlleles = 0;
for ( int x=0; x< v->nallele; x++)
{
f[x] /= sampleTotalDose;
if ( f[x] >= par::min_af )
++commonAlleles;
}
if ( commonAlleles>1 )
v->allelicVariation = true;
v->copyNumberVariation = false;
int commonCNV = 0;
map<int,int>::iterator ia = cnvCount.begin();
while ( ia != cnvCount.end() )
{
if ( (double)ia->second
/ (double)sampleTotalInd
>= par::min_af )
++commonCNV;
++ia;
}
if ( commonCNV>1 )
v->copyNumberVariation = true;
/////////////////////////////////
// Report to summary file
GOUT << setw(16) << v->name << " "
<< setw(12) << "CNV" << " ";
if ( v->copyNumberVariation )
GOUT << setw(12) << "yes" << "\n";
else
GOUT << setw(12) << "no" << "\n";
GOUT << setw(16) << v->name << " "
<< setw(12) << "ALLELIC" << " ";
if ( v->allelicVariation )
GOUT << setw(12) << "yes" << "\n";
else
GOUT << setw(12) << "no" << "\n";
GOUT << setw(16) << v->name << " "
<< setw(12) << "GCOUNT" << " "
<< setw(12) << sampleTotalInd << "\n";
if ( v->integerDosage )
GOUT << setw(16) << v->name << " "
<< setw(12) << "INTEGER" << " "
<< setw(12) << "Y" << "\n";
else
GOUT << setw(16) << v->name << " "
<< setw(12) << "INTEGER" << " "
<< setw(12) << "N" << "\n";
for (int a = 0; a < v->nallele; a++)
{
GOUT << setw(16) << v->name << " "
<< setw(12) << v->alleles[a] << " "
<< setw(12) << f[a] << "\n";
}
if ( v->integerDosage )
{
ia = cnvCount.begin();
while ( ia != cnvCount.end() )
{
GOUT << setw(16) << v->name << " "
<< setw(12) << "["+int2str(ia->first)+"]" << " "
<< setw(12)
<< (double)ia->second / (double)sampleTotalInd
<< "\n";
++ia;
}
////////////////////////////////////////////
// Display full Genotype counts (cases/all)
tit = typeCount.begin();
while ( tit != typeCount.end() )
{
string aname = "";
if ( (tit->first.a1.p2 == 0 ) )
aname += "null";
for (int z=0; z<tit->first.a1.p2; z++)
{
if ( tit->first.a1.p1 == -1 )
aname += par::out_missing_genotype;
else
aname += v->alleles[ tit->first.a1.p1 ];
}
aname += "/";
if ( (tit->first.a2.p2 == 0 ) )
aname += "null";
for (int z=0; z<tit->first.a2.p2; z++)
{
if ( tit->first.a2.p1 == -1 )
aname += par::out_missing_genotype;
else
aname += v->alleles[ tit->first.a2.p1 ];
}
GOUT << setw(16) << v->name << " "
<< setw(12) << aname << " ";
if ( par::bt )
GOUT << setw(12)
<< int2str(tit->second.p1)+":"+int2str(tit->second.p2)
<< "\n";
else
GOUT << setw(12)
<< tit->second.p1
<< "\n";
++tit;
}
}
///////////////////////////////
// Test for assocaition
if ( phenotypicVariation &&
( v->allelicVariation || v->copyNumberVariation ) )
{
// Place allelic variant and/or dosage information in
// covariate fields
par::clist = true;
Model * mJoint = NULL;
Model * mCNV = NULL;
Model * mAllelic = NULL;
if ( v->allelicVariation && v->copyNumberVariation )
mJoint = analyseModel(this,v,g,true,true);
if ( v->allelicVariation )
mAllelic = analyseModel(this,v,g,true,false);
if ( v->copyNumberVariation )
mCNV = analyseModel(this,v,g,false,true);
///////////////////////////////////////////////////////////////
// Extract results; for now we assume everything is biallelic
if ( mAllelic && mAllelic->isValid() )
{
vector_t b = mAllelic->getCoefs();
vector_t var = mAllelic->getVar();
vector_t pval = mAllelic->getPVals();
int term1 = par::clist_number + 1;
// double chisq = mAllelic->getStatistic();
// double pvalue = chiprobP(chisq,1);
GOUT << setw(16) << v->name << " "
<< setw(12) << "B(SNP)" << " "
<< setw(12) << b[ term1 ] << "\n";
GOUT << setw(16) << v->name << " "
<< setw(12) << "P(SNP)" << " "
<< setw(12) << pval[ term1 - 1 ] << "\n";
}
if ( mCNV && mCNV->isValid() )
{
vector_t b = mCNV->getCoefs();
vector_t var = mCNV->getVar();
vector_t pval = mCNV->getPVals();
int term1 = par::clist_number + 1;
// double chisq = mCNV->getStatistic();
// double pvalue = chiprobP(chisq,1);
GOUT << setw(16) << v->name << " "
<< setw(12) << "B(CNP)" << " "
<< setw(12) << b[ term1 ] << "\n";
GOUT << setw(16) << v->name << " "
<< setw(12) << "P(CNP)" << " "
<< setw(12) << pval[ term1 - 1 ] << "\n";
}
if ( mJoint && mJoint->isValid() )
{
int term1 = par::clist_number + 1;
int term2 = par::clist_number + 2;
vector_t b = mJoint->getCoefs();
vector_t var = mJoint->getVar();
vector_t p = mJoint->getPVals();
// A 2df test (joint test of two parameters)
vector_t h(2,0);
matrix_t H; // row = number of fixes; cols = np
sizeMatrix(H,2,mJoint->getNP());
H[0][term1] = H[1][term2] = 1;
double chisq = mJoint->isValid() ?
mJoint->linearHypothesis(H,h) : 0;
double pvalue = chiprobP(chisq,2);
GOUT << setw(16) << v->name << " "
<< setw(12) << "B(CNP|SNP)" << " "
<< setw(12) << b[term1] << "\n";
GOUT << setw(16) << v->name << " "
<< setw(12) << "P(CNP|SNP)" << " "
<< setw(12) << p[ term1 - 1 ] << "\n";
GOUT << setw(16) << v->name << " "
<< setw(12) << "B(SNP|CNP)" << " "
<< setw(12) << b[ term2 ] << "\n";
GOUT << setw(16) << v->name << " "
<< setw(12) << "P(SNP|CNP)" << " "
<< setw(12) << p[ term2 - 1 ] << "\n";
GOUT << setw(16) << v->name << " "
<< setw(12) << "P(SNP&CNP)" << " "
<< setw(12) << pvalue << "\n";
}
///////////////////////////////////////////
// No valid model
if ( ! ( mJoint || mAllelic || mCNV ) )
{
GOUT << setw(16) << v->name << " "
<< setw(12) << "SNP/CNP" << " "
<< setw(12) << "NA" << "\n";
}
//////////////////////////////////
// Clean-up
if ( mJoint )
delete mJoint;
if ( mAllelic )
delete mAllelic;
if ( mCNV )
delete mCNV;
} // End of association testing
} // Next generic variant
if ( true )
GOUT.close();
if ( par::gvar_verbose_association )