1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
|
/**********************************************************************
*
* hmm_f2.h
*
* copyright (c) 2001-7, Karl W Broman
*
* last modified Oct, 2007
* first written Feb, 2001
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License,
* version 3, as published by the Free Software Foundation.
*
* This program is distributed in the hope that it will be useful,
* but without any warranty; without even the implied warranty of
* merchantability or fitness for a particular purpose. See the GNU
* General Public License, version 3, for more details.
*
* A copy of the GNU General Public License, version 3, is available
* at http://www.r-project.org/Licenses/GPL-3
*
* C functions for the R/qtl package
*
* Contains: init_f2, emit_f2, step_f2, init_f2b, emit_f2b, step_f2b,
* calc_genoprob_f2, calc_genoprob_special_f2, sim_geno_f2, est_map_f2,
* argmax_geno_f2, errorlod_f2, calc_errorlod_f2, nrec2_f2,
* logprec_f2, est_rf_f2, calc_pairprob_f2, marker_loglik_f2
*
* These are the init, emit, and step functions plus
* all of the hmm wrappers for the F2 intercross.
*
* Genotype codes: 0=AA; 1=AB; 2=BB
* Phenotype codes: 0=missing; 1=AA; 2=AB; 3=BB; 4=not BB; 5=not AA
*
**********************************************************************/
double init_f2(int true_gen, int *cross_scheme);
double emit_f2(int obs_gen, int true_gen, double error_prob, int *cross_scheme);
double step_f2(int gen1, int gen2, double rf, double junk, int *cross_scheme);
double init_f2b(int true_gen, int *cross_scheme);
double emit_f2b(int obs_gen, int true_gen, double error_prob, int *cross_scheme);
double step_f2b(int gen1, int gen2, double rf, double junk, int *cross_scheme);
double nrec_f2b(int gen1, int gen2, double rf, int *cross_scheme);
void calc_genoprob_f2(int *n_ind, int *n_mar, int *geno,
double *rf, double *error_prob, double *genoprob);
void calc_genoprob_special_f2(int *n_ind, int *n_mar, int *geno,
double *rf, double *error_prob, double *genoprob);
void sim_geno_f2(int *n_ind, int *n_pos, int *n_draws, int *geno,
double *rf, double *error_prob, int *draws);
void est_map_f2(int *n_ind, int *n_mar, int *geno, double *rf,
double *error_prob, double *loglik, int *maxit,
double *tol, int *verbose);
void argmax_geno_f2(int *n_ind, int *n_pos, int *geno,
double *rf, double *error_prob, int *argmax);
double errorlod_f2(int obs, double *prob, double error_prob);
void calc_errorlod_f2(int *n_ind, int *n_mar, int *geno,
double *error_prob, double *genoprob,
double *errlod);
double nrec2_f2(int obs1, int obs2, double rf, int *cross_scheme);
double logprec_f2(int obs1, int obs2, double rf, int *cross_scheme);
void est_rf_f2(int *n_ind, int *n_mar, int *geno, double *rf,
int *maxit, double *tol);
void calc_pairprob_f2(int *n_ind, int *n_mar, int *geno,
double *rf, double *error_prob, double *genoprob,
double *pairprob);
void marker_loglik_f2(int *n_ind, int *geno,
double *error_prob, double *loglik);
/* end of hmm_f2.h */
|
