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comparison PsiCLASS-1.0.2/samtools-0.1.19/bcftools/fet.c @ 0:903fc43d6227 draft default tip

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author lsong10
date Fri, 26 Mar 2021 16:52:45 +0000
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1 #include <math.h>
2 #include <stdlib.h>
3
4 /* This program is implemented with ideas from this web page:
5 *
6 * http://www.langsrud.com/fisher.htm
7 */
8
9 // log\binom{n}{k}
10 static double lbinom(int n, int k)
11 {
12 if (k == 0 || n == k) return 0;
13 return lgamma(n+1) - lgamma(k+1) - lgamma(n-k+1);
14 }
15
16 // n11 n12 | n1_
17 // n21 n22 | n2_
18 //-----------+----
19 // n_1 n_2 | n
20
21 // hypergeometric distribution
22 static double hypergeo(int n11, int n1_, int n_1, int n)
23 {
24 return exp(lbinom(n1_, n11) + lbinom(n-n1_, n_1-n11) - lbinom(n, n_1));
25 }
26
27 typedef struct {
28 int n11, n1_, n_1, n;
29 double p;
30 } hgacc_t;
31
32 // incremental version of hypergenometric distribution
33 static double hypergeo_acc(int n11, int n1_, int n_1, int n, hgacc_t *aux)
34 {
35 if (n1_ || n_1 || n) {
36 aux->n11 = n11; aux->n1_ = n1_; aux->n_1 = n_1; aux->n = n;
37 } else { // then only n11 changed; the rest fixed
38 if (n11%11 && n11 + aux->n - aux->n1_ - aux->n_1) {
39 if (n11 == aux->n11 + 1) { // incremental
40 aux->p *= (double)(aux->n1_ - aux->n11) / n11
41 * (aux->n_1 - aux->n11) / (n11 + aux->n - aux->n1_ - aux->n_1);
42 aux->n11 = n11;
43 return aux->p;
44 }
45 if (n11 == aux->n11 - 1) { // incremental
46 aux->p *= (double)aux->n11 / (aux->n1_ - n11)
47 * (aux->n11 + aux->n - aux->n1_ - aux->n_1) / (aux->n_1 - n11);
48 aux->n11 = n11;
49 return aux->p;
50 }
51 }
52 aux->n11 = n11;
53 }
54 aux->p = hypergeo(aux->n11, aux->n1_, aux->n_1, aux->n);
55 return aux->p;
56 }
57
58 double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two)
59 {
60 int i, j, max, min;
61 double p, q, left, right;
62 hgacc_t aux;
63 int n1_, n_1, n;
64
65 n1_ = n11 + n12; n_1 = n11 + n21; n = n11 + n12 + n21 + n22; // calculate n1_, n_1 and n
66 max = (n_1 < n1_) ? n_1 : n1_; // max n11, for right tail
67 min = n1_ + n_1 - n;
68 if (min < 0) min = 0; // min n11, for left tail
69 *two = *_left = *_right = 1.;
70 if (min == max) return 1.; // no need to do test
71 q = hypergeo_acc(n11, n1_, n_1, n, &aux); // the probability of the current table
72 // left tail
73 p = hypergeo_acc(min, 0, 0, 0, &aux);
74 for (left = 0., i = min + 1; p < 0.99999999 * q; ++i) // loop until underflow
75 left += p, p = hypergeo_acc(i, 0, 0, 0, &aux);
76 --i;
77 if (p < 1.00000001 * q) left += p;
78 else --i;
79 // right tail
80 p = hypergeo_acc(max, 0, 0, 0, &aux);
81 for (right = 0., j = max - 1; p < 0.99999999 * q; --j) // loop until underflow
82 right += p, p = hypergeo_acc(j, 0, 0, 0, &aux);
83 ++j;
84 if (p < 1.00000001 * q) right += p;
85 else ++j;
86 // two-tail
87 *two = left + right;
88 if (*two > 1.) *two = 1.;
89 // adjust left and right
90 if (abs(i - n11) < abs(j - n11)) right = 1. - left + q;
91 else left = 1.0 - right + q;
92 *_left = left; *_right = right;
93 return q;
94 }
95
96 #ifdef FET_MAIN
97 #include <stdio.h>
98
99 int main(int argc, char *argv[])
100 {
101 char id[1024];
102 int n11, n12, n21, n22;
103 double left, right, twotail, prob;
104
105 while (scanf("%s%d%d%d%d", id, &n11, &n12, &n21, &n22) == 5) {
106 prob = kt_fisher_exact(n11, n12, n21, n22, &left, &right, &twotail);
107 printf("%s\t%d\t%d\t%d\t%d\t%.6g\t%.6g\t%.6g\t%.6g\n", id, n11, n12, n21, n22,
108 prob, left, right, twotail);
109 }
110 return 0;
111 }
112 #endif