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Searched defs:unfiltered_marker_ct (Results 1 – 15 of 15) sorted by relevance

/dports/biology/plink/plink-ng-79b2df8c/1.9/
H A Dplink_misc.c476 int32_t apply_cm_map(char* cm_map_fname, char* cm_map_chrname, uintptr_t unfiltered_marker_ct, uint… in apply_cm_map()
654 …_htable_size, char* marker_ids, uintptr_t max_marker_id_len, uintptr_t unfiltered_marker_ct, doubl… in update_marker_cms()
932 …er_id_htable_size, char* marker_ids, uintptr_t max_marker_id_len, uintptr_t unfiltered_marker_ct) { in update_marker_names()
1037 …_htable_size, char* marker_ids, uintptr_t max_marker_id_len, uintptr_t unfiltered_marker_ct, uintp… in update_marker_alleles()
1257 …_htable_size, char* marker_ids, uintptr_t max_marker_id_len, uintptr_t unfiltered_marker_ct, uintp… in flip_strand()
1711 uint32_t calc_plink_maxsnp(uint32_t unfiltered_marker_ct, uintptr_t* marker_exclude, uint32_t marke… in calc_plink_maxsnp()
1863 int32_t read_external_freqs(char* freqname, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclu… in read_external_freqs()
2224 int32_t load_ax_alleles(Two_col_params* axalleles, uintptr_t unfiltered_marker_ct, uintptr_t* marke… in load_ax_alleles()
3306 int32_t write_snplist(char* outname, char* outname_end, uintptr_t unfiltered_marker_ct, uintptr_t* … in write_snplist()
3377 int32_t write_var_ranges(char* outname, char* outname_end, uintptr_t unfiltered_marker_ct, uintptr_… in write_var_ranges()
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H A Dplink_filter.c318 …t do_exclude, char* marker_ids, uintptr_t max_marker_id_len, uintptr_t unfiltered_marker_ct, uintp… in extract_exclude_flag_norange()
894 …_no_variants, char* marker_ids, uintptr_t max_marker_id_len, uintptr_t unfiltered_marker_ct, uintp… in filter_qual_scores()
1022 uint32_t random_thin_markers(double thin_keep_prob, uintptr_t unfiltered_marker_ct, uintptr_t* mark… in random_thin_markers()
1049 int32_t random_thin_markers_ct(uint32_t thin_keep_ct, uintptr_t unfiltered_marker_ct, uintptr_t* ma… in random_thin_markers_ct()
1159 int32_t load_oblig_missing(FILE* bedfile, uintptr_t bed_offset, uintptr_t unfiltered_marker_ct, uin… in load_oblig_missing()
1587 …ffset, char* outname, char* outname_end, double mind_thresh, uintptr_t unfiltered_marker_ct, uintp… in mind_filter()
2490 … plink_maxfid, uint32_t plink_maxiid, uint32_t plink_maxsnp, uintptr_t unfiltered_marker_ct, uintp… in write_missingness_reports()
2876 …eport(char* outname, char* outname_end, double output_min_p, uintptr_t unfiltered_marker_ct, uintp… in hardy_report()
3065 uint32_t enforce_hwe_threshold(double hwe_thresh, uintptr_t unfiltered_marker_ct, uintptr_t* marker… in enforce_hwe_threshold()
3142 …orce_minor_allele_thresholds(double min_maf, double max_maf, uintptr_t unfiltered_marker_ct, uintp… in enforce_minor_allele_thresholds()
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H A Dplink_set.c588 int32_t extract_exclude_range(char* fname, uint32_t* marker_pos, uintptr_t unfiltered_marker_ct, ui… in extract_exclude_range()
992 int32_t define_sets(Set_info* sip, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude, uint3… in define_sets()
1690 …* sip, char* outname, char* outname_end, uint32_t marker_ct, uintptr_t unfiltered_marker_ct, uintp… in write_set()
1925 void unpack_set_unfiltered(uintptr_t marker_ct, uintptr_t unfiltered_marker_ct, uintptr_t* marker_e… in unpack_set_unfiltered()
2094 …act_set_union_unfiltered(Set_info* sip, uintptr_t* set_incl, uintptr_t unfiltered_marker_ct, uintp… in extract_set_union_unfiltered()
2120 …mpress(Set_info* sip, uintptr_t* set_incl, uintptr_t set_ct, uintptr_t unfiltered_marker_ct, uintp… in setdefs_compress()
H A Dplink_rserve.c33 …g, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct, uintptr_t unfiltered_marker_ct, uintp… in rserve_call()
H A Dplink_data.c74 …_major_to_snp_major(char* sample_major_fname, char* outname, uintptr_t unfiltered_marker_ct, uintp… in sample_major_to_snp_major()
208 uintptr_t unfiltered_marker_ct = 0; in load_map() local
421 uintptr_t unfiltered_marker_ct = 0; in load_bim() local
2488 int32_t update_marker_chroms(Two_col_params* update_chr, uintptr_t unfiltered_marker_ct, uintptr_t*… in update_marker_chroms()
2681 int32_t sort_and_write_bim(uint32_t* map_reverse, char* outname, uintptr_t unfiltered_marker_ct, ui… in sort_and_write_bim()
2766 …apfile, uint32_t map_cols, char* outname, char* outname_end, uintptr_t unfiltered_marker_ct, uintp… in load_sort_and_write_map()
3027 …t32_t mergex, uint32_t splitx_bound1, uint32_t splitx_bound2, uint32_t unfiltered_marker_ct, uintp… in merge_or_split_x()
5737 uintptr_t unfiltered_marker_ct = 0; in ped_to_bed() local
6414 uintptr_t unfiltered_marker_ct = 0; in lgen_to_bed() local
11463 …_size, char* recode_allele_name, char*** allele_missing_ptr, uintptr_t unfiltered_marker_ct, uintp… in recode_allele_load()
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H A Dplink_ld.c638 …2_t cur_uidx, Chrom_info* chrom_info_ptr, uint32_t chrom_code_end, uint32_t unfiltered_marker_ct) { in ld_prune_next_valid_chrom_start()
652 …ptr, uint32_t ld_window_size, uint32_t* cur_window_size_ptr, uintptr_t unfiltered_marker_ct, uintp… in ld_prune_start_chrom()
752 …p, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct, uintptr_t unfiltered_marker_ct, uintp… in ld_prune()
2182 …threads, Ld_info* ldip, FILE* bedfile, uintptr_t bed_offset, uintptr_t unfiltered_marker_ct, uintp… in ld_report_matrix()
5670 …threads, Ld_info* ldip, FILE* bedfile, uintptr_t bed_offset, uintptr_t unfiltered_marker_ct, uintp… in ld_report_regular()
6315 …p, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct, uintptr_t unfiltered_marker_ct, uintp… in show_tags()
7081 …p, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct, uintptr_t unfiltered_marker_ct, uintp… in haploview_blocks()
7886 …p, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct, uintptr_t unfiltered_marker_ct, uintp… in twolocus()
10407 …p, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct, uintptr_t unfiltered_marker_ct, uintp… in indep_pairphase()
11332 …fset, char* outname, char* outname_end, double output_min_p, uintptr_t unfiltered_marker_ct, uintp… in test_mishap()
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H A Dplink_lasso.c432 …* pheno_nm, const uintptr_t* covar_nm, uintptr_t bed_offset, uintptr_t unfiltered_marker_ct, uintp… in lasso_lambda()
994 …ile, uintptr_t bed_offset, char* outname, char* outname_end, uintptr_t unfiltered_marker_ct, uintp… in lasso()
H A Dplink.c204 …lexxxx_recode(uint32_t allelexxxx, char** marker_allele_ptrs, uint32_t unfiltered_marker_ct, uintp… in allelexxxx_recode()
258 …rse_bin(uintptr_t* marker_reverse, uintptr_t* marker_exclude, uint32_t unfiltered_marker_ct, uint3… in calc_marker_reverse_bin()
277 void swap_reversed_marker_alleles(uintptr_t unfiltered_marker_ct, uintptr_t* marker_reverse, char**… in swap_reversed_marker_alleles()
325 uintptr_t unfiltered_marker_ct = 0; in plink() local
H A Dplink_family.c683 …k_maxiid, uint32_t plink_maxsnp, uint32_t allow_no_variants, uintptr_t unfiltered_marker_ct, uintp… in mendel_error_scan()
1730 …fset, char* outname, char* outname_end, double output_min_p, uintptr_t unfiltered_marker_ct, uintp… in tdt_poo()
1983 …e output_min_p, uint32_t mtest_adjust, double adjust_lambda, uintptr_t unfiltered_marker_ct, uintp… in tdt()
3799 …e output_min_p, uint32_t mtest_adjust, double adjust_lambda, uintptr_t unfiltered_marker_ct, uintp… in dfam()
5393 …ile, uintptr_t bed_offset, char* outname, char* outname_end, uintptr_t unfiltered_marker_ct, uintp… in qfam()
5982 …ile, uintptr_t bed_offset, char* outname, char* outname_end, uintptr_t unfiltered_marker_ct, uintp… in make_pseudocontrols()
H A Dplink_glm.c91 …can_conditions(char* condition_mname, char* condition_fname, uintptr_t unfiltered_marker_ct, uintp… in glm_scan_conditions()
3554 …tr, Range_list* tests_range_list_ptr, uint32_t mtest_adjust, uintptr_t unfiltered_marker_ct, uintp… in glm_common_init()
4053 … double pfilter, double output_min_p, uint32_t mtest_adjust, uintptr_t unfiltered_marker_ct, uintp… in glm_linear_assoc_set_test()
4362 …e output_min_p, uint32_t mtest_adjust, double adjust_lambda, uintptr_t unfiltered_marker_ct, uintp… in glm_linear_assoc()
5616 … double pfilter, double output_min_p, uint32_t mtest_adjust, uintptr_t unfiltered_marker_ct, uintp… in glm_logistic_assoc_set_test()
5896 …e output_min_p, uint32_t mtest_adjust, double adjust_lambda, uintptr_t unfiltered_marker_ct, uintp… in glm_logistic_assoc()
7052 … ci_size, double ci_zt, double pfilter, double output_min_p, uintptr_t unfiltered_marker_ct, uintp… in glm_linear_nosnp()
7915 … ci_size, double ci_zt, double pfilter, double output_min_p, uintptr_t unfiltered_marker_ct, uintp… in glm_logistic_nosnp()
H A Dplink_calc.c4509 …ds, FILE* bedfile, uintptr_t bed_offset, uint32_t marker_ct, uintptr_t unfiltered_marker_ct, uintp… in calc_genome()
6235 int32_t load_distance_wts(char* distance_wts_fname, uintptr_t unfiltered_marker_ct, char* marker_id… in load_distance_wts()
6367 …d, char* distance_wts_fname, uint32_t distance_wts_noheader, uintptr_t unfiltered_marker_ct, uintp… in calc_rel()
6985 …ar* outname_end, uint64_t calculation_type, Rel_info* relip, uintptr_t unfiltered_marker_ct, uintp… in calc_pca()
7453 …ibm(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, uintptr_t unfiltered_marker_ct, uintp… in calc_ibm()
7568 …nce_exp, uint64_t calculation_type, uint32_t dist_calc_type, uintptr_t unfiltered_marker_ct, uintp… in calc_distance()
8258 …ds, FILE* bedfile, uintptr_t bed_offset, uint32_t marker_ct, uintptr_t unfiltered_marker_ct, uintp… in calc_cluster_neighbor()
H A Dplink_assoc.c5600 … double pfilter, double output_min_p, uint32_t mtest_adjust, uintptr_t unfiltered_marker_ct, uintp… in model_assoc_set_test()
5997 …e output_min_p, uint32_t mtest_adjust, double adjust_lambda, uintptr_t unfiltered_marker_ct, uintp… in model_assoc()
7777 … double pfilter, double output_min_p, uint32_t mtest_adjust, uintptr_t unfiltered_marker_ct, uintp… in qassoc_set_test()
8086 …e output_min_p, uint32_t mtest_adjust, double adjust_lambda, uintptr_t unfiltered_marker_ct, uintp… in qassoc()
9968 …e output_min_p, uint32_t mtest_adjust, double adjust_lambda, uintptr_t unfiltered_marker_ct, uintp… in testmiss()
11005 …e output_min_p, uint32_t mtest_adjust, double adjust_lambda, uintptr_t unfiltered_marker_ct, uintp… in cmh_assoc()
11373 …fset, char* outname, char* outname_end, double output_min_p, uintptr_t unfiltered_marker_ct, uintp… in cmh2_assoc()
11625 …fset, char* outname, char* outname_end, double output_min_p, uintptr_t unfiltered_marker_ct, uintp… in homog_assoc()
H A Dplink_dosage.c563 uintptr_t unfiltered_marker_ct = 0; in plink1_dosage() local
H A Dplink_homozyg.c2426 …hp, FILE* bedfile, uintptr_t bed_offset, uint32_t marker_ct, uintptr_t unfiltered_marker_ct, uintp… in calc_homozyg()
H A Dplink_common.c4977 …const Chrom_info* chrom_info_ptr, const uintptr_t* marker_exclude, uint32_t unfiltered_marker_ct) { in single_chrom_start()
8278 …cate_non_autosomal_markers(const Chrom_info* chrom_info_ptr, uintptr_t unfiltered_marker_ct, const… in conditional_allocate_non_autosomal_markers()