Subroutines

A - B - C - D - E - F - G - H - I - J - K - L - M - N - O - P - Q - R - S - T - U - V - W - X - Y - Z - 0 - 1 - 2 - 3 - 4 - 5 - 6 - 7 - 8 - 9

A

add_animal_genea add_effcov add_effcov_multi add_general_mean add_general_mean_multi add_haplotype_effect add_other_continue_traits_as_cov add_polygenic_effect add_polygenic_effect_multi add_qtleffect add_qtleffect_multi add_qtlinteraction allocate_vector_ analyse analyse_cuda ancetre

B

bilan_shared_haplo build_incidence_matrix

C

calcul_corcd calcul_phases_symmax2sat_dam calcul_phases_symmax2sat_sire calcul_rang calcul_y_cd change_interaction_effect change_qtleffect change_qtleffect_multi check_allocate check_cd check_change_maker_windows check_HWE check_map check_marker_name check_recombination_sire check_traits_and_fathers check_typage chromo_is_select clean_lrt_solution cli_get_analyse cli_get_family cli_get_haplotype cli_get_nqtl cli_get_nsim cli_get_optimization cli_get_parameters_file cli_is_calcul_cd cli_is_debug cli_is_estimate_thresholds cli_is_hdam cli_is_help cli_is_help_panalyse cli_is_help_paramsim cli_is_nopoly cli_is_nsim cli_is_permute cli_is_print_all cli_is_quiet cli_is_simulation cli_is_transcriptomic_data cli_is_verbose cli_is_xmloutput cli_print_help cli_print_qtlmap_version confbin confusion confusion_between_qtl_and_effect confusion_multi_type1 confusion_type1 contingence contingence_cox contingence_ldla copy copy_dataset copy_description_type copy_incidence_desc courbe_lin_ldla create_grid_file_2QTL create_sparse_W CREATE_STRUCT_GRAND_PARENT CREATE_STRUCT_PARENT

D

debug_write_incidence dget_str

E

end_analyse_DA_1QTL end_analyse_gen end_analyse_lin_gen end_analyse_linear end_analyse_modlin end_analyse_modlin_cox end_analyse_modlin_ldla end_analyse_multitrait end_analyse_parameterfile end_analyse_unitrait_1QTL end_analyse_unitrait_2qtl end_contingence end_dataset end_incidence end_incidence_multi end_output_handler end_position end_sub_1qtl end_sub_1qtl end_sub_2qtl estim_cholesky extend extendListCorrAnim extendListNa extendListTrio EXTRACT

F

fget_str file_exist fill_nonull_elements fixe_structure_model free_internal_struct free_internal_struct_ldla funct_0qtl funct_0qtl funct_0qtl_discret_family funct_0qtl_discret_unitrait funct_0qtl_family funct_0qtl_modlin funct_0qtl_modlin_cox funct_0qtl_modlin_family funct_0qtl_modlin_ldla_family funct_1car_2qtl funct_1car_2qtl_family funct_1qtl funct_1qtl funct_1qtl_discret_family funct_1qtl_discret_unitrait funct_1qtl_family funct_1qtl_modlin funct_1qtl_modlin_cox funct_1qtl_modlin_family funct_1qtl_modlin_ldla funct_1qtl_modlin_ldla_family funct_mcar_0qtl funct_mcar_0qtl_family funct_mcar_1qtl funct_mcar_1qtl_family

G

gen_loop_opti_nqtl_multi gen_opti_nqtl gen_opti_nqtl_cuda gen_opti_nqtl_multi GET get_arg get_binary_name get_correlations get_dx get_eff_paternal_and_total get_gradient get_gradient_optim_fam get_gradient_optim_fam_multi get_gradient_optim_fam_sire get_h_from_w get_ilong get_incidence_reduit get_ind_pheno get_int get_int_char get_inv_residual_covariance_matrix get_inv_residual_covariance_matrix get_inv_residual_covariance_matrix_cd get_inv_residual_covariance_matrix_LU get_inv_residual_covariance_matrix_LU_cd get_key_value get_key_value get_listProgenies get_long_step_morgan get_maxnbgenotypedam get_maxnpo get_name_analyse get_nb_arg get_npo get_pdd_at_mark get_pheno get_pos get_precision get_real get_real_char get_summary_panalyse get_type_data_analyse get_value get_value_optim_fam get_value_optim_fam_multi get_value_optim_fam_sire getglobalprob getprob_lin getprobld_lin global_gamete

H

haplotype haplotype_external haplotype_offspring haplotype_offspring_v1 haplotype_SNP haplotype_SYMMAX2SAT_SNP haplotype_V1 haplotype_V2 haplotype_V3 help_panalyse

I

iget_str init_analyse_DA_1QTL init_analyse_gen init_analyse_lin_gen init_analyse_linear init_analyse_modlin init_analyse_modlin_cox init_analyse_modlin_ldla init_analyse_multitrait init_analyse_unitrait_1QTL init_analyse_unitrait_2QTL init_contingence init_dataset_1car init_dataset_ncar init_genotype_simul init_incidence init_incidence_multi INIT_INTERNAL_MAP_STRUCTURE init_model_struct init_output_handler init_perf_animal init_permutation init_pheno init_position init_random init_simul_genealogy init_simul_marker init_startpoint init_sub_1qtl init_sub_1qtl init_sub_2qtl init_traits_simul init_workstruct initialise_struct_internal initialize_dev_generic_keys initialize_qtlmap_context initialize_tocartha_context internal_read_file is_multitrait_analysis

K

key_exist key_exist key_exist_file

L

likelihood_discret_h0_family likelihood_discret_hn_family likelihood_empty likelihood_h0_family likelihood_hn_family likelihood_ncar_h0_family likelihood_ncar_h0_family_LU likelihood_ncar_h0_family_withcd likelihood_ncar_h0_LU likelihood_ncar_h0_LU_family_withcd likelihood_ncar_hn_family likelihood_ncar_hn_family_LU likelihood_ncar_hn_family_withcd likelihood_ncar_hn_LU likelihood_ncar_hn_LU_family_withcd liste_gamete liste_haplo liste_haplo_complet liste_shared_haplo local_gamete log_debug_genea log_descriptif_genealogy log_descriptif_traits log_infoqtldefinedbyuser log_marker_description log_simulation_message

M

m_qtlmap_output_xml/print_pded_xml manage_data manage_simulator_traits MATH_QTLMAP_F01ADF MATH_QTLMAP_F03ABF MATH_QTLMAP_G01AAF MATH_QTLMAP_G01EAF MATH_QTLMAP_G01EBF MATH_QTLMAP_G01ECF MATH_QTLMAP_G01EEF MATH_QTLMAP_G01FAF MATH_QTLMAP_G03ACF MATH_QTLMAP_G05EHF MATH_QTLMAP_INFO MATH_QTLMAP_INVDETMAT MATH_QTLMAP_INVDETMATSYM MATH_QTLMAP_LOWERTAIL_BETA MATH_QTLMAP_M01CAF MATH_QTLMAP_M01DAF MATH_QTLMAP_S15ADF MATH_QTLMAP_S15AEF matmul_incidence minimizing_e04jyf minimizing_funct minimizing_funct_family minimizing_funct_family_multi minimizing_funct_family_sire minimizing_lbfgs minimizing_nlopt model_lin_h0 model_lin_hn model_optim_family model_optim_h0 model_optim_hn model_optim_multi_family model_optim_multi_h0 model_optim_multi_h0_LU model_optim_multi_hn model_optim_multi_hn_LU model_optim_multi_LU model_XT_V_X model_XT_X modele_heteroscedastic modele_homoscedastic

N

name_optim need_normalize_data new new_lrt_solution next_word next_word_char normal normalize_data

O

opti_0qtl opti_0qtl opti_0qtl_cuda opti_0qtl_discret_unitrait opti_0qtl_linear opti_0qtl_modlin opti_0qtl_modlin_cox opti_0qtl_modlin_ldla opti_0qtl_multi opti_1car_2qtl opti_1qtl opti_1qtl_discret_unitrait opti_1qtl_modlin opti_1qtl_modlin_cox opti_1qtl_modlin_ldla opti_2qtl_linear_interaction opti_DA_0qtl opti_DA_1qtl opti_mcar_0qtl opti_mcar_1qtl opti_multitrait_DA opti_multitrait_modlin opti_multitraits opti_nqtl opti_nqtl_cuda opti_nqtl_multi opti_unitrait opti_unitrait_discret opti_unitrait_incidence opti_unitrait_incidence_cuda opti_unitrait_interaction opti_unitrait_modlin opti_unitrait_modlin_cox opti_unitrait_modlin_new optinit optinit_da optinit_mcar

P

parse_real_array pdd_at_position pdd_at_position_multi pded pded_v5 pded_v5_kd pded_v5_optim pdegm pdegm_snp pdegp pdegp_snp perform_DA_1qtl point_gamete precision prepinc print_allelic_origin print_coeff_linear_combination print_coeff_linear_combination_max print_confusion print_courbe_LRT print_dam_phase print_end_multitraits print_end_unitrait print_freqall print_incidence_solution print_incidence_solution_risk_factor print_LRT print_LRT_2QTL print_lrt_solution print_maximum_LRT print_offspring_phase print_pat_mat_effect_2QTL print_paternal_maternal_effect print_pded print_residual_correlation print_resume_simulation print_resume_simulation_2 print_sire_phase print_start_multitrait_DA print_start_multitraits print_start_unitrait print_summary_analyse print_summary_panalyse print_test_nuisances print_transcriptome print_transcriptome_H0 print_transcriptome_Struct_famille print_transmission_allele proba_haplo_complet probin

Q

quantile QUANTILE1

R

read_analyse_file read_attributes_discrete_trait read_correlation_matrix read_genealogy read_genotype read_map read_model read_perf_by_column read_perf_by_line read_qtl_effect_on_trait read_simulation_file read_traits recup release release_copy_incidence_desc release_data release_description_type release_incidence_solution release_lrt_solution release_model_trait release_ws REMOVE

S

scale_variables_dam set_absi set_allele_info_vector set_allocation set_allocation set_base_and_step set_corresponding_vector set_corrxinc set_count_discrete set_estfem set_estime set_file_output set_filter_optim set_haplo_final set_haplo_for_ldla set_haplotype_offspring_context set_MR set_ntnivmax set_optimization set_phasm set_phasp set_pheno set_proportion_discrete set_RHS set_RHS_V set_simulation_genealogy set_simulation_marker set_simulation_qtl set_simulation_simultraits set_simulation_traits set_soglia set_solution set_solution_hypothesis0 set_solution_hypothesis0 set_solution_hypothesis0 set_solution_hypothesis0 set_solution_hypothesis0 set_solution_hypothesis0 set_solution_hypothesis1 set_solution_hypothesis1 set_solution_hypothesis1 set_solution_hypothesis1 set_solution_hypothesis1 set_solution_hypothesis1 set_solution_hypothesis1 set_solution_hypothesis2 set_tab_ibs set_VInv set_xml_output setting_alloc_pdd sim_carte sim_genea sim_genea_F2_BC sim_genea_outbread sim_perf_shuffling sim_perf_tirage sim_QTL sim_transform_discret sim_typ solve_lin solve_lin_dgefs solvesymmax2sat sort_haplo stop_application stop_on_error str

T

test_lin test_lin test_lin_cox test_lin_ldla test_module_isymmax2sat1 test_nuisances test_print_haplotype to_integer tri_haplo_complet

W

W write_genea write_map write_perf write_simulation_file write_typ

X

xaldane xosambi

A - B - C - D - E - F - G - H - I - J - K - L - M - N - O - P - Q - R - S - T - U - V - W - X - Y - Z - 0 - 1 - 2 - 3 - 4 - 5 - 6 - 7 - 8 - 9