tsp_individual_multi::DNA tsp_individual_multi::translateToDnaPhenotypicOrdinal(const DNA trait){
DNA ordinal;
DNA tmp;
for(int i=0;i<trait.size();i++){
tmp.push_back(i);
}
ordinal.resize(trait.size());
for(int i=0;i<trait.size();i++){
ordinal[i] = tmp[trait[i]];
tmp.erase(tmp.begin() + trait[i]);
}
return ordinal;
}
PermutationTest& PermutationTest::permute (DNA *dna_in, const int niter, Random &ran) {
dna = dna_in;
int i, j, k, pos;
/* Find out which sites are bi-allelic segregating */
/* (segregating for short) */
char state1, state2;
vector<bool> segregating (dna->lseq);
for (i = 0; i < dna->lseq; i++) {
segregating[i] = false;
state1 = (*dna) [0][i];
for (j = 1; j < dna->nseq; j++)
if ( (*dna) [j][i] != state1) {
state2 = (*dna) [j][i];
segregating[i] = true;
j++;
for (; j < dna->nseq; j++)
if ( (*dna) [j][i] != state1 && (*dna) [j][i] != state2) {
/* Tri-allelic segregating */
segregating[i] = false;
break;
}
break;
}
}
/* Count number of segregating sites */
int nseg = 0;
for (i = 0; i < dna->lseq; i++)
if (segregating[i]) {
nseg++;
}
if (nseg == 0) {
error ("No segregating sites found");
}
/* Copy segregating sites to a new DNA object */
sdna.resize (dna->nseq, nseg);
vector<double> d (nseg, 0.0);
for (i = 0, pos = 0; i < dna->lseq; i++)
if (segregating[i]) {
for (j = 0; j < dna->nseq; j++) {
sdna[j][pos] = (*dna) [j][i];
}
d[pos] = (double) i;
++pos;
}
/* Calculate frequency statistics */
vector<double> F (sdna.lseq, 1.0); /* F is the marginal frequency of the dna[0][i] (A) allele at site i */
vector<double> four (4, 0.0); /* G[i][j] is the frequency of AB (G[i][j][0]), Ab (1), aB (2), ab (3) */
LowerTriangularMatrix< vector<double> > G (sdna.lseq, four);
for (i = 0; i < sdna.lseq; i++) {
state1 = sdna[0][i];
for (j = 1; j < sdna.nseq; j++)
if (sdna[j][i] == state1) {
F[i]++;
}
F[i] /= (double) sdna.nseq;
}
for (i = 0; i < sdna.lseq; i++)
for (j = 0; j < i; j++) {
state1 = sdna[0][i];
state2 = sdna[0][j];
for (k = 0; k < sdna.nseq; k++) {
if (sdna[k][i] == state1 && sdna[k][j] == state2) {
++G[i][j][0];
} else if (sdna[k][i] == state1 && sdna[k][j] != state2) {
++G[i][j][1];
} else if (sdna[k][i] != state1 && sdna[k][j] == state2) {
++G[i][j][2];
} else if (sdna[k][i] != state1 && sdna[k][j] != state2) {
++G[i][j][3];
} else {
warning ("Unexpected choice");
}
}
for (k = 0; k < 4; k++) {
G[i][j][k] /= (double) sdna.nseq;
}
}
/* Calculate LD statistics for pairs of sites */
LowerTriangularMatrix<double> A (nseg, 0.0);
LowerTriangularMatrix<double> B (nseg, 0.0);
LowerTriangularMatrix<double> C (nseg, 0.0);
Matrix<double> D (nseg, nseg, 0.0);
double temp;
// ofstream out("__out.txt");
// char tab = '\t';
// out << "locusA" << tab << "locusB" << tab << "rsq" << tab << "Dprime" << tab << "G4" << "dist" << endl;
for (i = 0; i < nseg; i++) {
for (j = 0; j < i; j++) {
temp = G[i][j][0] - F[i] * F[j];
A[i][j] = pow (temp, 2.0) / (F[i] * (1. - F[i]) * F[j] * (1. - F[j]) );
B[i][j] = (temp < 0.0) ? -temp / MIN (F[i] * F[j], (1. - F[i]) * (1. - F[j]) ) : temp / MIN (F[i] * (1. - F[j]), (1. - F[i]) * F[j]);
C[i][j] = (G[i][j][0] > 0.0 && G[i][j][1] > 0.0 && G[i][j][2] > 0.0 && G[i][j][3] > 0.0) ? 1.0 : 0.0;
D[i][j] = D[j][i] = d[i] - d[j];
// out << i << tab << j << tab << A[i][j] << tab << B[i][j] << tab << C[i][j] << tab << D[i][j] << endl;
}
}
// out.close();
/* Calculate remaining statistics for correlation coefficients */
double Abar, Bbar, Cbar, Dbar;
double Adev, Bdev, Cdev, Ddev;
Abar = Bbar = Cbar = Dbar = Adev = Bdev = Cdev = Ddev = 0.0;
double ctr = 0.0;
for (i = 0; i < nseg; i++)
for (j = 0; j < i; j++, ctr++) {
Abar += A[i][j];
Bbar += B[i][j];
Cbar += C[i][j];
Dbar += D[i][j];
}
Abar /= ctr;
Bbar /= ctr;
Cbar /= ctr;
Dbar /= ctr;
for (i = 0; i < nseg; i++)
for (j = 0; j < i; j++) {
Adev += pow (A[i][j] - Abar, 2.0);
Bdev += pow (B[i][j] - Bbar, 2.0);
Cdev += pow (C[i][j] - Cbar, 2.0);
Ddev += pow (D[i][j] - Dbar, 2.0);
}
/* Perform the permutation tests */
double a, b, c, pa, pb, pc;
double PA, PB, PC, dist;
a = b = c = 0.0;
for (j = 0; j < nseg; j++)
for (k = 0; k < j; k++) {
a += A[j][k] * D[j][k];
b += B[j][k] * D[j][k];
c += C[j][k] * D[j][k];
}
double Aadd = ctr * Abar * Dbar;
double Adiv = sqrt (Adev * Ddev);
double Badd = ctr * Bbar * Dbar;
double Bdiv = sqrt (Bdev * Ddev);
double Cadd = ctr * Cbar * Dbar;
double Cdiv = sqrt (Cdev * Ddev);
a -= Aadd;
a /= Adiv;
b -= Badd;
b /= Bdiv;
c -= Cadd;
c /= Cdiv;
PA = PB = PC = 0.0;
vector<int> order (sdna.lseq);
vector<int> pool (sdna.lseq);
for (i = 0; i < niter; i++) {
for (j = 0; j < nseg; j++) {
pool[j] = j;
}
for (j = nseg - 1; j >= 0; j--) {
pos = ran.discrete (0, j);
order[j] = pool[pos];
pool[pos] = pool[j];
}
pa = pb = pc = 0.0;
for (j = 0; j < nseg; j++)
for (k = 0; k < j; k++) {
dist = D[order[j]][order[k]];
pa += A[j][k] * dist;
pb += B[j][k] * dist;
pc += C[j][k] * dist;
}
pa -= Aadd;
pa /= Adiv;
pb -= Badd;
pb /= Bdiv;
pc -= Cadd;
pc /= Cdiv;
if (pa <= a) {
++PA;
}
if (pb <= b) {
++PB;
}
if (pc >= c) {
++PC;
}
}
p[0] = (PA + 1.) / (double) (niter + 1);
v[0] = a;
p[1] = (PB + 1.) / (double) (niter + 1);
v[1] = b;
p[2] = (PC + 1.) / (double) (niter + 1);
v[2] = c;
if (coutput) {
printResults();
}
return *this;
}