/*
hap_freq - array to store haplotype frequencies
gl1 - GLs for site1 for all "n" individuals
gl2 - GLs for site2 for all "n" individuals
maf1 - minor allele frequency at site1
maf2 - minor allele frequency at site2
n_ind - number of individuals
log_scale - are GLs in log scale?
*/
uint64_t haplo_freq(double hap_freq[4], double **gl1, double **gl2, double maf1, double maf2, uint64_t n_ind, bool log_scale){
uint64_t i;
double hap_freq_last[4];
if(maf1 < 0 || maf1 > 1 || maf2 < 0 || maf2 > 1)
error("__FUNCTION__", "invalid allele frequencies");
// Initialize haplotype frequencies
hap_freq[0] = (1 - maf1) * (1 - maf2); // P_BA
hap_freq[1] = (1 - maf1) * maf2; // P_Ba
hap_freq[2] = maf1 * (1 - maf2); // P_bA
hap_freq[3] = maf1 * maf2; // P_ba
// iteration
for(i = 0; i < ITER_MAX; i++) {
double eps = 0;
memcpy(hap_freq_last, hap_freq, 4 * sizeof(double));
if(log_scale)
pair_freq_iter_log(hap_freq, gl1, gl2, n_ind);
else
pair_freq_iter(hap_freq, gl1, gl2, n_ind);
for (uint64_t j = 0; j < 4; j++) {
double x = fabs(hap_freq[j] - hap_freq_last[j]);
if (x > eps) eps = x;
}
if(eps < EPSILON)
break;
}
return i;
}
double bcf_pair_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4])
{
const bcf1_t *b[2];
int i, j, n_smpl;
double *pdg[2], flast[4], r, f0[2];
// initialize others
if (b0->n_smpl != b1->n_smpl) return -1; // different number of samples
n_smpl = b0->n_smpl;
b[0] = b0; b[1] = b1;
f[0] = f[1] = f[2] = f[3] = -1.;
if (b[0]->n_alleles < 2 || b[1]->n_alleles < 2) return -1; // one allele only
pdg[0] = get_pdg3(b0); pdg[1] = get_pdg3(b1);
if (pdg[0] == 0 || pdg[1] == 0) {
free(pdg[0]); free(pdg[1]);
return -1;
}
// set the initial value
f0[0] = est_freq(n_smpl, pdg[0]);
f0[1] = est_freq(n_smpl, pdg[1]);
f[0] = (1 - f0[0]) * (1 - f0[1]); f[3] = f0[0] * f0[1];
f[1] = (1 - f0[0]) * f0[1]; f[2] = f0[0] * (1 - f0[1]);
// iteration
for (j = 0; j < ITER_MAX; ++j) {
double eps = 0;
memcpy(flast, f, 4 * sizeof(double));
pair_freq_iter(n_smpl, pdg, f);
for (i = 0; i < 4; ++i) {
double x = fabs(f[i] - flast[i]);
if (x > eps) eps = x;
}
if (eps < EPS) break;
}
// free
free(pdg[0]); free(pdg[1]);
{ // calculate r^2
double p[2], q[2], D;
p[0] = f[0] + f[1]; q[0] = 1 - p[0];
p[1] = f[0] + f[2]; q[1] = 1 - p[1];
D = f[0] * f[3] - f[1] * f[2];
r = sqrt(D * D / (p[0] * p[1] * q[0] * q[1]));
// printf("R(%lf,%lf,%lf,%lf)=%lf\n", f[0], f[1], f[2], f[3], r);
if (_isnan(r)) r = -1.;
}
return r;
}
