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
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
|
#ifndef __PLINK_LD_H__
#define __PLINK_LD_H__
// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
// Christopher Chang.
//
// This program is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
//
// 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 for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program. If not, see <http://www.gnu.org/licenses/>.
#include "plink_set.h"
#define LD_MATRIX_SQ 1
#define LD_MATRIX_SQ0 2
#define LD_MATRIX_TRI 3
#define LD_MATRIX_SHAPEMASK 3
#define LD_MATRIX_BIN 4
#define LD_MATRIX_BIN4 8
#define LD_MATRIX_SPACES 0x10
#define LD_R2 0x20
#define LD_INTER_CHR 0x40
#define LD_REPORT_GZ 0x80
#define LD_INPHASE 0x100
#define LD_D 0x200
#define LD_DPRIME 0x400
#define LD_DPRIME_SIGNED 0x800
#define LD_DX (LD_D | LD_DPRIME | LD_DPRIME_SIGNED)
#define LD_WITH_FREQS 0x1000
#define LD_YES_REALLY 0x2000
#define LD_PRUNE_PAIRWISE 0x4000
#define LD_PRUNE_PAIRPHASE 0x8000
#define LD_PRUNE_KB_WINDOW 0x10000
#define LD_IGNORE_X 0x20000
#define LD_WEIGHTED_X 0x40000
#define LD_SNP_LIST_FILE 0x80000
#define LD_BLOCKS_NO_PHENO_REQ 0x100000
#define LD_BLOCKS_NO_SMALL_MAX_SPAN 0x200000
#define LD_FLIPSCAN_VERBOSE 0x400000
#define LD_SHOW_TAGS_LIST_ALL 0x800000
#define LD_SHOW_TAGS_MODE2 0x1000000
typedef struct {
double prune_last_param; // VIF or r^2 threshold
double window_cm;
double window_r2;
double blocks_min_maf;
double blocks_inform_frac;
double flipscan_thresh;
double show_tags_r2;
char* snpstr;
char* show_tags_fname;
Range_list snps_rl;
uint32_t modifier;
uint32_t prune_window_size;
uint32_t prune_window_incr;
uint32_t window_size;
uint32_t window_bp;
uint32_t blocks_max_bp;
// need two values here to replicate > vs. >= inconsistency in Haploview
uint32_t blocks_strong_lowci_outer;
uint32_t blocks_strong_lowci;
uint32_t blocks_strong_highci;
uint32_t blocks_recomb_highci;
uint32_t flipscan_window_size;
uint32_t flipscan_window_bp;
uint32_t show_tags_bp;
} Ld_info;
// fast epistasis test is really similar to LD scan so we put it in the same
// place
#define EPI_FAST 1
#define EPI_FAST_CASE_ONLY 2
#define EPI_FAST_NO_UEKI 4
#define EPI_FAST_BOOST 8
#define EPI_FAST_JOINT_EFFECTS 0x10
#define EPI_FAST_NO_P_VALUE 0x20
#define EPI_REG 0x40
#define EPI_SET_BY_SET 0x80
#define EPI_SET_BY_ALL 0x100
#define EPI_HWE_MIDP 0x200
typedef struct {
uint32_t modifier;
uint32_t case_only_gap;
double epi1;
double epi2;
uint32_t je_cellmin;
// twolocus() handles --ld too
char* ld_mkr1;
char* ld_mkr2;
char* twolocus_mkr1;
char* twolocus_mkr2;
char* summary_merge_prefix;
uint32_t summary_merge_ct;
} Epi_info;
#define CLUMP_ALLOW_OVERLAP 1
#define CLUMP_VERBOSE 2
#define CLUMP_INDEX_FIRST 4
#define CLUMP_REPLICATE 8
#define CLUMP_BEST 0x10
typedef struct {
uint32_t modifier;
uint32_t fname_ct;
uint32_t bp_radius; // distance must be less than or equal to this
uint32_t range_border;
char* fnames_flattened;
char* annotate_flattened;
char* snpfield_search_order;
char* pfield_search_order;
char* range_fname;
double p1;
double p2;
double r2;
} Clump_info;
void ld_epi_init(Ld_info* ldip, Epi_info* epi_ip, Clump_info* clump_ip);
void ld_epi_cleanup(Ld_info* ldip, Epi_info* epi_ip, Clump_info* clump_ip);
int32_t ld_prune(Ld_info* ldip, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude, uintptr_t* marker_reverse, char* marker_ids, uintptr_t max_marker_id_len, Chrom_info* chrom_info_ptr, double* set_allele_freqs, uint32_t* marker_pos, uintptr_t unfiltered_sample_ct, uintptr_t* founder_info, uintptr_t* sex_male, char* outname, char* outname_end, uint32_t hh_exists);
int32_t flipscan(Ld_info* ldip, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude, uintptr_t* marker_reverse, char* marker_ids, uintptr_t max_marker_id_len, uint32_t plink_maxsnp, char** marker_allele_ptrs, uintptr_t max_marker_allele_len, Chrom_info* chrom_info_ptr, double* set_allele_freqs, uint32_t* marker_pos, uintptr_t unfiltered_sample_ct, uintptr_t* pheno_nm, uintptr_t* pheno_c, uintptr_t* founder_info, uintptr_t* sex_male, char* outname, char* outname_end, uint32_t hh_exists);
int32_t ld_report(pthread_t* threads, Ld_info* ldip, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude, uintptr_t* marker_reverse, char* marker_ids, uintptr_t max_marker_id_len, uint32_t plink_maxsnp, char** marker_allele_ptrs, uintptr_t max_marker_allele_len, double* set_allele_freqs, Chrom_info* chrom_info_ptr, uint32_t* marker_pos, double* marker_cms, uintptr_t unfiltered_sample_ct, uintptr_t* founder_info, uint32_t parallel_idx, uint32_t parallel_tot, uintptr_t* sex_male, char* outname, char* outname_end, uint32_t hh_exists);
int32_t show_tags(Ld_info* ldip, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude, uintptr_t* marker_reverse, char* marker_ids, uintptr_t max_marker_id_len, uint32_t plink_maxsnp, uint32_t* marker_pos, Chrom_info* chrom_info_ptr, uintptr_t unfiltered_sample_ct, uintptr_t* founder_info, uintptr_t* sex_male, char* outname, char* outname_end, uint32_t hh_exists);
int32_t haploview_blocks(Ld_info* ldip, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude, char* marker_ids, uintptr_t max_marker_id_len, uint32_t* marker_pos, Chrom_info* chrom_info_ptr, double* set_allele_freqs, uintptr_t unfiltered_sample_ct, uintptr_t* founder_info, uintptr_t* pheno_nm, uintptr_t* sex_male, char* outname, char* outname_end, uint32_t hh_exists);
int32_t twolocus(Epi_info* epi_ip, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude, uintptr_t* marker_reverse, char* marker_ids, uintptr_t max_marker_id_len, uint32_t plink_maxsnp, char** marker_allele_ptrs, Chrom_info* chrom_info_ptr, uintptr_t unfiltered_sample_ct, uintptr_t* sample_exclude, uintptr_t sample_ct, uintptr_t* pheno_nm, uint32_t pheno_nm_ct, uint32_t pheno_ctrl_ct, uintptr_t* pheno_c, uintptr_t* sex_male, char* outname, char* outname_end, uint32_t hh_exists);
int32_t epistasis_report(pthread_t* threads, Epi_info* epi_ip, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude, uintptr_t* marker_reverse, char* marker_ids, uintptr_t max_marker_id_len, uint32_t* marker_pos, uint32_t plink_maxsnp, Chrom_info* chrom_info_ptr, uintptr_t unfiltered_sample_ct, uintptr_t* pheno_nm, uint32_t pheno_nm_ct, uint32_t ctrl_ct, uintptr_t* pheno_c, double* pheno_d, uint32_t parallel_idx, uint32_t parallel_tot, char* outname, char* outname_end, double output_min_p, double glm_vif_thresh, Set_info* sip);
int32_t indep_pairphase(Ld_info* ldip, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude, uintptr_t* marker_reverse, char* marker_ids, uintptr_t max_marker_id_len, Chrom_info* chrom_info_ptr, double* set_allele_freqs, uint32_t* marker_pos, uintptr_t unfiltered_sample_ct, uintptr_t* founder_info, uintptr_t* sex_male, char* outname, char* outname_end, uint32_t hh_exists);
int32_t epi_summary_merge(Epi_info* epi_ip, char* outname, char* outname_end);
int32_t test_mishap(FILE* bedfile, uintptr_t bed_offset, char* outname, char* outname_end, double output_min_p, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude, uintptr_t* marker_reverse, uintptr_t marker_ct, char* marker_ids, uintptr_t max_marker_id_len, uint32_t plink_maxsnp, char** marker_allele_ptrs, double min_maf, Chrom_info* chrom_info_ptr, uintptr_t unfiltered_sample_ct, uintptr_t* sample_exclude, uintptr_t sample_ct);
void set_test_score(uintptr_t marker_ct, double chisq_threshold, uint32_t set_max, double* chisq_arr, uint32_t** ld_map, uint32_t* cur_setdef, double* sorted_chisq_buf, uint32_t* sorted_marker_idx_buf, uint32_t* proxy_arr, uint32_t* raw_sig_ct_ptr, uint32_t* final_sig_ct_ptr, double* set_score_ptr);
int32_t set_test_common_init(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, char* outname, char* outname_end, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude_orig, uintptr_t marker_ct_orig, char* marker_ids, uintptr_t max_marker_id_len, uintptr_t* marker_reverse, double* orig_chisq, Set_info* sip, Chrom_info* chrom_info_ptr, uintptr_t unfiltered_sample_ct, uintptr_t* sex_male, uintptr_t* founder_pnm, uint32_t ld_ignore_x, uint32_t hh_exists, const char* flag_descrip, uintptr_t* marker_ct_ptr, uintptr_t** marker_exclude_ptr, uintptr_t** set_incl_ptr, uint32_t** marker_idx_to_uidx_ptr, uint32_t*** setdefs_ptr, uintptr_t* set_ct_ptr, uint32_t* max_sigset_size_ptr, uint32_t*** ld_map_ptr, double* chisq_threshold_ptr, double** orig_set_scores_ptr, double** sorted_chisq_buf_ptr, uint32_t** sorted_marker_idx_buf_ptr, uint32_t** proxy_arr_ptr, uintptr_t** perm_adapt_set_unstopped_ptr, uint32_t** perm_2success_ct_ptr, uint32_t** perm_attempt_ct_ptr, uintptr_t** unstopped_markers_ptr);
void compute_set_scores(uintptr_t marker_ct, uintptr_t perm_vec_ct, uintptr_t set_ct, double* chisq_matrix, double* orig_set_scores, double* sorted_chisq_buf, uint32_t* sorted_marker_idx_buf, uint32_t* proxy_arr, uint32_t** setdefs, uint32_t** ld_map, Aperm_info* apip, double chisq_threshold, double adaptive_ci_zt, uint32_t first_adapt_check, uint32_t perms_done, uint32_t set_max, uintptr_t* perm_adapt_set_unstopped, uint32_t* perm_2success_ct, uint32_t* perm_attempt_ct);
int32_t write_set_test_results(char* outname, char* outname_end2, Set_info* sip, uint32_t** ld_map, uint32_t** setdefs, uintptr_t* set_incl, uintptr_t set_ct, uintptr_t marker_ct_orig, uintptr_t marker_ct, uint32_t* marker_idx_to_uidx, char* marker_ids, uintptr_t max_marker_id_len, uint32_t* perm_2success_ct, uint32_t* perm_attempt_ct, uint32_t mtest_adjust, uint32_t perm_count, double pfilter, double output_min_p, double chisq_threshold, double* orig_stats, double* sorted_chisq_buf, uint32_t* sorted_marker_idx_buf, uint32_t* proxy_arr);
int32_t clump_reports(FILE* bedfile, uintptr_t bed_offset, char* outname, char* outname_end, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude, uintptr_t marker_ct, char* marker_ids, uintptr_t max_marker_id_len, uint32_t plink_maxsnp, uint32_t* marker_pos, char** marker_allele_ptrs, uintptr_t* marker_reverse, Chrom_info* chrom_info_ptr, uintptr_t unfiltered_sample_ct, uintptr_t* founder_info, Clump_info* clump_ip, uintptr_t* sex_male, uint32_t hh_exists);
#endif // __PLINK_LD_H__
|
