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//////////////////////////////////////////////////////////////////
// //
// PLINK (c) 2005-2006 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 "plink.h"
#include "options.h"
using namespace std;
vector<Z> Plink::calcLocusIBD(Individual * p1, Individual * p2, Z I)
{
// ** TODO ** -- development code -- lots of possible speedups here.
// 1) Remove I as an argument
// 2) Now no need to calculate all probabilities -- just do the three required for that
// particular locus
// Store calculated P(M|Z) here
vector<Z> ZL(nl);
// Locus counter
int l = 0;
//////////////////////////////
// All SNPs in the scan region
for (int l2=par::run_start; l2<=par::run_end; l2++)
{
/////////////////////
// Allele frequencies
double p = locus[l2]->freq;
double q = 1 - p;
// Na = # alleles = 2N where N is number of individuals
double Na = locus[l]->nm;
double x = p * Na;
double y = q * Na;
/////////////////////////////////////////////////
// Assign P(M|Z) based on genotype for each SNP
bool a1 = p1->one[l2];
bool a2 = p1->two[l2];
bool b1 = p2->one[l2];
bool b2 = p2->two[l2];
// Assign unit vector if either genotype is missing
if ( ( a1 && (!a2) ) ||
( b1 && (!b2) ) )
{
ZL[l].z0 = ZL[l].z1 = ZL[l].z2 = 1;
l++;
continue;
}
if ( a1 )
{
if ( a2 )
{
if ( b1 )
{
if ( b2 )
{
// aa, aa
ZL[l].z0 = q*q*q*q
* ( (y-1)/y * (y-2)/y * (y-3)/y * (Na/(Na-1)) * (Na/(Na-2)) * (Na/(Na-3)) );
ZL[l].z1 = q*q*q * ( (y-1)/y * (y-2)/y * Na/(Na-1) * Na/(Na-2));
ZL[l].z2 = q*q * ( (y-1)/y * Na/(Na-1));
}
}
else
{
if ( b2 )
{
// aa, Aa
ZL[l].z0 = 2*p*q*q*q
* ( (y-1)/y * (y-2)/y * (Na/(Na-1)) * (Na/(Na-2)) * (Na/(Na-3)) );
ZL[l].z1 = p*q*q * ((y-1)/y * Na/(Na-1) * Na/(Na-2));
ZL[l].z2 = 0;
}
else
{
// aa, AA
ZL[l].z0 = p*p*q*q
* ( (x-1)/x * (y-1)/y * (Na/(Na-1)) * (Na/(Na-2)) * (Na/(Na-3)) );
ZL[l].z1 = 0;
ZL[l].z2 = 0;
}
}
}
}
else
{
if ( a2 )
{
if ( b1 )
{
if ( b2 )
{
// Aa, aa
ZL[l].z0 = 2*p*q*q*q
* ( (y-1)/y * (y-2)/y * (Na/(Na-1)) * (Na/(Na-2)) * (Na/(Na-3)) );
ZL[l].z1 = p*q*q * ((y-1)/y * Na/(Na-1) * Na/(Na-2));
ZL[l].z2 = 0;
}
}
else
{
if ( b2 )
{
// Aa, Aa
ZL[l].z0 = 4*p*p*q*q
* ( (x-1)/x * (y-1)/y * (Na/(Na-1)) * (Na/(Na-2)) * (Na/(Na-3)) );
ZL[l].z1 = p*p*q
* ( (x-1)/x * Na/(Na-1) * Na/(Na-2) )
+ p*q*q
* ((y-1)/y * Na/(Na-1) * Na/(Na-2));
ZL[l].z2 = 2*p*q * Na/(Na-1) ;
}
else
{
// Aa, AA
ZL[l].z0 = 2*p*p*p*q
* ( (x-1)/x * (x-2)/x * (Na/(Na-1)) * (Na/(Na-2)) * (Na/(Na-3)) );
ZL[l].z1 = p*p*q
* ( (x-1)/x * Na/(Na-1) * Na/(Na-2) );
ZL[l].z2 = 0;
}
}
}
else
{
if ( b1 )
{
if ( b2 )
{
// AA, aa
ZL[l].z0 = p*p*q*q
* ( (x-1)/x * (y-1)/y * (Na/(Na-1)) * (Na/(Na-2)) * (Na/(Na-3)) );
ZL[l].z1 = 0;
ZL[l].z2 = 0;
}
}
else
{
if ( b2 )
{
// AA, Aa
ZL[l].z0 = 2*p*p*p*q
* ( (x-1)/x * (x-2)/x * (Na/(Na-1)) * (Na/(Na-2)) * (Na/(Na-3)) );
ZL[l].z1 = p*p*q
* ( (x-1)/x * Na/(Na-1) * Na/(Na-2) );
ZL[l].z2 = 0;
}
else
{
// AA, AA
ZL[l].z0 = p*p*p*p
* ( (x-1)/x * (x-2)/x * (x-3)/x * (Na/(Na-1)) * (Na/(Na-2)) * (Na/(Na-3)));
ZL[l].z1 = p*p*p
* ( (x-1)/x * (x-2)/x * Na/(Na-1) * Na/(Na-2));
ZL[l].z2 = p*p
* ( (x-1)/x * Na/(Na-1));
}
}
}
}
/////////////////////////////////////
// Fudge factor for genotyping error
if ( ZL[l].z1 < 0.0001 )
{
ZL[l].z1 = 0.0001;
double S = ZL[l].z0 + ZL[l].z1 + ZL[l].z2;
ZL[l].z0 /= S;
ZL[l].z1 /= S;
ZL[l].z2 /= S;
}
/////////////////
// Next SNP
l++;
}
return ZL;
}
// ////////////////////////////////////////////
// // 2. Allow for possible genotyping error
// // sum_{all possible true genotypes} P(observed G|true G) P(true G |IBD)
// // double e = 0.005;
// // double f = 0.001;
// // double ER_AA_AA__AA_AA = 1- 2e - 2f - 2e*f - e*e - f*f;
// // double ER_AA_AB__AA_AA = e;
// // double ER_AA_BB__AA_AA = f;
// // double ER_AB_AA__AA_AA = e;
// // double ER_AB_AB__AA_AA = e*e;
// // double ER_AB_BB__AA_AA = e*f;
// // double ER_BB_AA__AA_AA = f;
// // double ER_BB_AB__AA_AA = e*f;
// // double ER_BB_BB__AA_AA = f*f;
// // double ER_AA_AA__AA_AB = e;
// // double ER_AA_AB__AA_AB = 1 - 3*e - 2*e*e - 2*e*f - f;
// // double ER_AA_BB__AA_AB = e;
// // double ER_AB_AA__AA_AB = e*e;
// // double ER_AB_AB__AA_AB = e;
// // double ER_AB_BB__AA_AB = e*e;
// // double ER_BB_AA__AA_AB = f*e;
// // double ER_BB_AB__AA_AB = f;
// // double ER_BB_BB__AA_AB = f*e;
// // Sum over all possible true genotypes P(Observed G | True G) P(True G |IBD = 1)
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