double MothurFisher::hyper_323(double n11, double n1_, double n_1, double n){
try {
return(exp(lnbico(n1_,n11)+lnbico(n-n1_,n_1-n11)-lnbico(n,n_1)));
}catch(exception& e) {
m->errorOut(e, "MothurFisher", "hyper_323");
exit(1);
}
}
double MotifSearch::matrix_score() {
double ms = 0.0;
float* freq_matrix = new float[4 * motif.ncols()];
motif.calc_freq_matrix(freq_matrix);
int nc = motif.ncols();
int w = motif.get_width();
double sc[] = {0.0,0.0,0.0,0.0};
for(int i = 0; i < 4 * nc; i += 4) {
for(int j = 0; j < 4; j++) {
ms += gammaln((double) freq_matrix[i + j] + params.pseudo[j]);
sc[j] += freq_matrix[i + j];
}
}
delete [] freq_matrix;
ms -= nc * gammaln((double) motif.number() + params.npseudo);
for (int j = 0; j < 4; j++)
ms -= sc[j] * log(params.backfreq[j]);
/*
This factor arises from a modification of the model of Liu, et al
in which the background frequencies of DNA bases are taken to be
constant for the organism under consideration
*/
double vg = 0.0;
ms -= lnbico(w - 2, nc - 2);
for(int j = 0; j < 4; j++)
vg += gammaln(params.pseudo[j]);
vg -= gammaln((double) (params.npseudo));
ms -= ((double) nc * vg);
return ms;
}
double prob_overlap(int x, int s1, int s2, int n) {
assert(x <= s1);
assert(x <= s2);
assert(s1 <= n);
assert(s2 <= n);
if(x == 0)
return 1;
int m1 = min(s1, s2);
int m2 = max(s1, s2);
double ret, lt;
if(x > m1 - x) {
ret = 0.0;
for(int i = x; i <= m1; i++) {
lt = lnbico(m1, i) + lnbico(n - m1, m2 - i) - lnbico(n, m2);
ret += lt;
}
return ret;
} else {
ret = 1.0;
for(int i = 0; i < x; i++) {
lt = lnbico(m1, i) + lnbico(n - m1, m2 - i) - lnbico(n, m2);
ret -= lt;
}
}
return ret;
}
double log_prob_overlap(int x, int s1, int s2, int n) {
assert(x <= s1);
assert(x <= s2);
assert(s1 <= n);
assert(s2 <= n);
if(x == 0)
return 0;
int m1 = min(s1, s2);
int m2 = max(s1, s2);
double ret = 0.0, lt;
for(int i = x; i <= m1; i++) {
lt = lnbico(m1, i) + lnbico(n - m1, m2 - i) - lnbico(n, m2);
if(! ret)
ret = lt;
else
ret = logsum(ret, lt);
if(lt < ret - 5) break;
}
return ret;
}