| add_annotation_nu_params |
Source code
|
| add_annotation_params |
Source code
|
| add_annotation_shift_params |
Source code
|
| add_genotypes2bagea_annotation_mat |
Source code
|
| add_heritability_quantile_mat |
Source code
|
| add_summary_stats2bagea_annotation_mat |
Source code
|
| all_theta_b_alphai_gene_indices_to_cluster_node |
Source code
|
| assemble_cov |
Source code
|
| assemble_data_mats |
Source code
|
| calc_Eb2_XtX_trace |
Source code
|
| calc_Eu_ak_optimized |
Source code
|
| calc_Eu_ak_via_theta |
Source code
|
| calc_Eu_alpha_via_theta |
Source code
|
| calc_Eu_alphai_via_theta |
Source code
Source code
|
| calc_Eu_alphai_via_theta_only_second |
Source code
|
| calc_Eu_alphai_via_theta_only_second_withpreindexing |
Source code
|
| calc_Eu_alphai_via_theta_vectorized |
Source code
|
| calc_Eu_b_via_theta |
Source code
|
| calc_Eu_b_via_theta4eigen |
Source code
|
| calc_Eu_chi2j_via_theta |
Source code
|
| calc_Eu_delta_via_theta |
Source code
|
| calc_Eu_gamma |
Source code
|
| calc_Eu_gamma_func_via_theta |
Source code
|
| calc_Eu_gammai_via_Eu_ak |
Source code
|
| calc_Eu_gammai_via_Eu_ak_only_second |
Source code
|
| calc_Eu_kappa_via_theta |
Source code
|
| calc_Eu_kappa_via_theta_only_second |
Source code
|
| calc_Eu_kappa_via_theta_vectorized |
Source code
|
| calc_Eu_lambda2_via_theta |
Source code
|
| calc_Eu_lambda_via_theta |
Source code
|
| calc_Eu_nu_via_theta |
Source code
|
| calc_Eu_omega_via_theta |
Source code
|
| calc_Eu_tau2_via_theta |
Source code
|
| calc_Eu_upsilon_via_theta |
Source code
|
| calc_Eu_upsilon_via_theta_list |
Source code
|
| calc_L_alpha |
Source code
|
| calc_L_alpha_minus_star |
Source code
|
| calc_L_alpha_observed |
Source code
|
| calc_L_b |
Source code
|
| calc_L_b_observed |
Source code
|
| calc_L_b_star_part_2 |
Source code
|
| calc_L_b_star_part_2_only_diag |
Source code
|
| calc_L_global |
Source code
|
| calc_L_lambda |
Source code
|
| calc_L_upsilon |
Source code
|
| calc_L_y_observed |
Source code
|
| calc_L_y_observed4eigen |
Source code
|
| calc_L_y_slow |
Source code
|
| calc_L_z_observed |
Source code
|
| calc_L_z_observed4eigen |
Source code
|
| calc_ZtSigma_invZ |
Source code
|
| calc_diag_mtCm |
Source code
|
| calc_diag_mtCm_flipped |
Source code
|
| calc_diag_mtCm_flipped2 |
Source code
|
| calc_diag_mtCm_flipped_preindexed |
Source code
|
| calc_diag_mtCm_flipped_preindexed2 |
Source code
|
| calc_f_b_from_natural |
Source code
|
| calc_fast_cov_solve |
Source code
|
| calc_g_a1_via_theta |
Source code
|
| calc_g_ak_via_theta |
Source code
|
| calc_g_alpha |
Source code
|
| calc_g_alpha_via_theta |
Source code
|
| calc_g_alphai_via_Eu_gammai |
Source code
|
| calc_g_alphai_via_Eu_gammai_Eu_kappa |
Source code
|
| calc_g_alphai_via_theta |
Source code
Source code
|
| calc_g_b |
Source code
|
| calc_g_b_from_natural |
Source code
|
| calc_g_b_via_Eu_alphai |
Source code
|
| calc_g_b_via_Eu_wshift_nu |
Source code
|
| calc_g_b_via_Eu_wshift_nu_fast |
Source code
|
| calc_g_b_via_theta |
Source code
|
| calc_g_b_via_theta4eigen |
Source code
|
| calc_g_b_via_theta4eigen_only_diag |
Source code
|
| calc_g_b_via_thetaOld |
Source code
|
| calc_g_chi2j_via_Eu |
Source code
|
| calc_g_chi2j_via_theta |
Source code
|
| calc_g_delta_via_Eu |
Source code
|
| calc_g_delta_via_theta |
Source code
|
| calc_g_kappa |
Source code
|
| calc_g_kappa_via_Eu_tau2 |
Source code
|
| calc_g_kappa_via_theta |
Source code
|
| calc_g_lambda |
Source code
|
| calc_g_lambda2 |
Source code
|
| calc_g_lambda2_via_theta |
Source code
|
| calc_g_lambda_via_Eu_lambda2 |
Source code
|
| calc_g_lambda_via_theta |
Source code
|
| calc_g_nu_via_Eu |
Source code
|
| calc_g_nu_via_theta |
Source code
|
| calc_g_omega_via_Eu |
Source code
|
| calc_g_omega_via_Eu_upsilon |
Source code
|
| calc_g_omega_via_theta |
Source code
|
| calc_g_tau2 |
Source code
|
| calc_g_tau2_via_theta |
Source code
|
| calc_g_upsilon_via_Eu |
Source code
|
| calc_g_upsilon_via_Eu_chi2j |
Source code
|
| calc_g_upsilon_via_theta_list |
Source code
|
| calc_g_y_b |
Source code
|
| calc_g_y_canonical |
Source code
|
| calc_g_y_lambda |
Source code
|
| calc_he |
Source code
|
| calc_he_test |
Source code
|
| calc_natural_from_theta_b |
Source code
|
| calc_pseudo_inverse |
Source code
|
| calc_rescaled_omega_estimates |
Source code
|
| calc_theta_ak |
Source code
|
| calc_theta_ak_via_Eu |
Source code
|
| calc_theta_alpha |
Source code
|
| calc_theta_alpha_ak_kappa_via_Eu |
Source code
|
| calc_theta_alpha_ak_via_Eu |
Source code
|
| calc_theta_alpha_ak_via_Eugammai |
Source code
|
| calc_theta_alpha_ak_via_EugammaiTimesEu_alphai_vect_only_second_ |
Source code
|
| calc_theta_alpha_ak_via_Eugammai_vect |
Source code
|
| calc_theta_alpha_ak_via_Eugammai_vect_only_second |
Source code
|
| calc_theta_alpha_ak_via_Eugammai_vect_only_second_with_preindexi |
Source code
Source code
|
| calc_theta_alpha_aks_via_Eu |
Source code
|
| calc_theta_alpha_via_Eu |
Source code
|
| calc_theta_alphai_ak_kappa_via_Eu |
Source code
|
| calc_theta_alphai_ak_via_Eu |
Source code
|
| calc_theta_alphai_kappa_via_Eu_gammai_Eu_alphai |
Source code
|
| calc_theta_alphai_kappa_via_Eu_gammai_Eu_alphai_from_dt |
Source code
|
| calc_theta_alphai_kappa_via_Eu_gammai_Eu_alphai_second_from_mat |
Source code
|
| calc_theta_alphai_kappa_via_Eu_gammai_Eu_alphai_second_from_mat_ |
Source code
|
| calc_theta_alphai_kappa_via_Eu_gammai_Eu_alphai_vect |
Source code
|
| calc_theta_alphai_via_Eu_gammai |
Source code
|
| calc_theta_alphai_via_Eu_gammai_Eu_kappa |
Source code
|
| calc_theta_alphai_via_Eu_gammai_Eu_kappa_second |
Source code
|
| calc_theta_alphai_via_Eu_gammai_Eu_kappa_second_with_preindexing |
Source code
|
| calc_theta_alphai_via_Eu_gammai_second |
Source code
|
| calc_theta_b |
Source code
|
| calc_theta_b_alpha |
Source code
|
| calc_theta_b_alpha_via_Eu |
Source code
|
| calc_theta_b_from_natural |
Source code
|
| calc_theta_b_nu_via_Eu_vectorized_fast |
Source code
|
| calc_theta_b_nu_via_Eu_vectorized_slow |
Source code
|
| calc_theta_b_omega_via_Eu_nu |
Source code
|
| calc_theta_b_omega_via_Eu_nu_vectorized_fast |
Source code
|
| calc_theta_b_via_Eu |
Source code
|
| calc_theta_bi_alphai_via_Eu |
Source code
|
| calc_theta_bi_alphai_via_Eu_wshift_nu |
Source code
|
| calc_theta_bi_nu_via_Eu_wshift |
Source code
|
| calc_theta_bi_via_Eu |
Source code
|
| calc_theta_bi_via_Eu_diag |
Source code
|
| calc_theta_bi_via_Eu_wshift_nu |
Source code
|
| calc_theta_bi_via_Eu_wshift_nu_diag |
Source code
|
| calc_theta_chi2j |
Source code
|
| calc_theta_delta |
Source code
|
| calc_theta_kappa |
Source code
|
| calc_theta_kappaj_tau2_via_Eu_kappaj |
Source code
|
| calc_theta_kappaj_via_Eu_tau2 |
Source code
|
| calc_theta_lambda |
Source code
|
| calc_theta_lambda2 |
Source code
|
| calc_theta_lambda_via_Eu |
Source code
|
| calc_theta_lambdai_lambda2_via_Eu_lambdai |
Source code
|
| calc_theta_nu |
Source code
|
| calc_theta_omegas_deltas_via_Eu |
Source code
|
| calc_theta_omegas_upsilon_via_Eu |
Source code
|
| calc_theta_omegas_via_Eu |
Source code
|
| calc_theta_omegas_via_Eu_upsilon |
Source code
|
| calc_theta_tau2 |
Source code
|
| calc_theta_upsilon |
Source code
|
| calc_theta_upsilon_chi2j_via_Eu |
Source code
|
| calc_theta_upsilon_via_Eu_chi2j |
Source code
|
| calc_theta_y_b |
Source code
|
| calc_theta_y_b_via_Eu |
Source code
|
| calc_theta_y_b_via_Eu_sqrt_abs |
Source code
|
| calc_theta_y_canonical |
Source code
|
| calc_theta_y_lambda |
Source code
|
| calc_theta_y_lambda_via_Eu |
Source code
|
| calc_theta_y_lambda_via_Eu_svd |
Source code
|
| calc_theta_z_b |
Source code
|
| calc_theta_z_b_via_Eu |
Source code
|
| calc_theta_z_lambda |
Source code
|
| calc_theta_z_lambda_via_Eu |
Source code
|
| calc_theta_z_lambda_via_Eu_svd |
Source code
|
| calc_y_canonical |
Source code
|
| calculate_L_ak |
Source code
|
| calculate_L_minus_ak_alpha_split |
Source code
|
| calculate_ZtSigma_invZ_list |
Source code
|
| calculate_determinant_sym |
Source code
|
| calculate_missing_variance |
Source code
|
| calculate_woodbury_inversion |
Source code
|
| calculate_woodbury_inversion_sym |
Source code
|
| check_E_el |
Source code
|
| check_E_gamma_el |
Source code
|
| check_E_gaussian_el |
Source code
|
| check_Eu_omega_list_fromoutput |
Source code
|
| check_bagea_observed_data |
Source code
Source code
|
| check_bagea_output |
Source code
Source code
|
| check_bedops |
Source code
|
| check_boolean |
Source code
Source code
|
| check_class |
Source code
Source code
|
| check_core_nrs |
Source code
|
| check_gene_dat_list |
Source code
|
| check_global_E_list |
Source code
|
| check_hyperparameter_list |
Source code
|
| check_input |
Source code
|
| check_installation |
Source code
|
| check_logicalmatrix |
Source code
Source code
|
| check_matrix |
Source code
Source code
|
| check_notnan |
Source code
Source code
|
| check_numeric |
Source code
Source code
|
| check_obs_el |
Source code
|
| check_paramgreaterthan0 |
Source code
|
| check_path |
Source code
Source code
|
| check_pos |
Source code
Source code
|
| check_posinteger |
Source code
Source code
|
| check_range |
Source code
|
| check_round_indices |
Source code
|
| check_scalar |
Source code
Source code
|
| check_settings_list_obs |
Source code
|
| check_settings_list_obs1KG |
Source code
|
| check_string |
Source code
Source code
|
| check_theta_gamma |
Source code
|
| check_vector |
Source code
Source code
|
| check_yty_on_node_list |
Source code
|
| clusterApply_or_envApply |
Source code
|
| clusterApply_or_envApply2 |
Source code
|
| clusterCall_or_envCall |
Source code
|
| clusterEvalQ_or_envEvalQ |
Source code
|
| clusterExport_or_envExport |
Source code
|
| collapse_Eu_kappa_vect |
Source code
|
| combine_genotype_mats |
Source code
|
| combine_genotype_mats_and_remove_lowmaf_snps |
Source code
|
| compare_lists |
Source code
|
| compare_lists_test |
Source code
|
| do_simulation |
Source code
|
| expand_Eu_b_list |
Source code
|
| extract_D_mat_info |
Source code
|
| extract_snp_names |
Source code
|
| filter_on_minpvalue |
Source code
|
| get_E_list |
Source code
|
| get_Eu_b_table |
Source code
|
| get_Eu_kappa_vect_from_update_outl |
Source code
|
| get_L_lambda_from_node |
Source code
|
| get_L_y_obs_from_node |
Source code
|
| get_XtX |
Source code
|
| get_all_Ls_from_node |
Source code
|
| get_all_theta_alphai_ak |
Source code
|
| get_all_theta_alphai_ak_k |
Source code
|
| get_all_theta_alphai_star_from_vect_form |
Source code
|
| get_all_theta_b_alphai_gene_indices |
Source code
|
| get_all_theta_b_alphai_second |
Source code
|
| get_all_theta_b_alphai_vect |
Source code
|
| get_alphasplits |
Source code
|
| get_bagea_E_ak_convergence_matrix |
Source code
|
| get_cluster_size |
Source code
|
| get_commonsnp_filepath |
Source code
|
| get_data_container_environment |
Source code
|
| get_diag_from_inv_decompose |
Source code
|
| get_download_cmdstr |
Source code
|
| get_gene_cluster_index |
Source code
|
| get_gene_cluster_index_fromrange_obj |
Source code
|
| get_gene_indices_vec |
Source code
|
| get_gene_indices_vec_boundaries |
Source code
|
| get_gene_lengths |
Source code
|
| get_gene_names_splits_fromrange_obj |
Source code
|
| get_genewise_param_list |
Source code
|
| get_globalE_list |
Source code
|
| get_global_L_sum |
Source code
|
| get_global_param_list |
Source code
|
| get_local_L_sum |
Source code
|
| get_lowmaf_snps |
Source code
|
| get_mapping_mat_colnames |
Source code
|
| get_matcher_vectors |
Source code
|
| get_metaannotation_filepath |
Source code
|
| get_nsnps_per_gene |
Source code
|
| get_nu_names |
Source code
|
| get_numgenes_persplit |
Source code
|
| get_numgenes_persplit_fromrange_obj |
Source code
|
| get_objsize_on_node |
Source code
|
| get_objsize_on_node2 |
Source code
|
| get_objsizes |
Source code
|
| get_objsizes2 |
Source code
|
| get_objsizes3 |
Source code
|
| get_objsizes4 |
Source code
|
| get_objsizes5 |
Source code
|
| get_objsizes6 |
Source code
|
| get_objsizes7 |
Source code
|
| get_objsizes_full_stack |
Source code
|
| get_objsizes_full_stack_wnamespace |
Source code
|
| get_objsizes_round |
Source code
|
| get_objsizes_round2 |
Source code
|
| get_objsizes_round3 |
Source code
|
| get_params_for_global_cov |
Source code
|
| get_pickrell_ldblocks_filepath |
Source code
|
| get_preprocess_expression_mats |
Source code
|
| get_s3_download_cmdstr |
Source code
|
| get_settingsout_list_bagea |
Source code
|
| get_settingsout_list_obs |
Source code
|
| get_settingsout_list_obs1KG |
Source code
|
| get_shift_mat_melted_on_node |
Source code
|
| get_shift_mat_melted_on_node_sham |
Source code
|
| get_snpfreq_annot |
Source code
|
| get_tmpfile |
Source code
|
| get_tss_filepath |
Source code
|
| get_unique_matcher_mat |
Source code
Source code
|
| get_variance_from_maf |
Source code
|
| has_unique_names |
Source code
Source code
|
| initialize_alphai_kappa |
Source code
|
| initialize_concat_local_E_lists |
Source code
|
| initialize_contiguous_vectors |
Source code
|
| initialize_index_mats |
Source code
|
| initialize_index_range_mappings |
Source code
|
| initialize_lambda1nrho1_for_approx_mode |
Source code
|
| initialize_parameters |
Source code
|
| initialize_theta_alphai_star_vect_l |
Source code
|
| initialize_traces |
Source code
|
| inititalize_constant_theta_first_cols |
Source code
|
| install_1KG_data |
Source code
|
| install_external_data |
Source code
|
| install_gtex |
Source code
|
| intersect_expression_genes_fully |
Source code
|
| intersect_order_preserving |
Source code
|
| intersect_snps_fully |
Source code
|
| is.pos |
Source code
Source code
|
| is.scalar |
Source code
Source code
|
| is_ascending_integer_vec |
Source code
|
| is_gwas_summary_stats_tbl |
Source code
|
| load_Eu_alphai_second_list_to_cluster_node |
Source code
|
| load_Eu_alphai_second_to_cluster_node |
Source code
|
| load_Eu_alphai_to_cluster_node |
Source code
|
| load_all_genotype_mats |
Source code
|
| load_alphai_star_second_to_cluster_node |
Source code
|
| load_as |
Source code
Source code
|
| load_data_from_cluster_node |
Source code
|
| load_data_to_cluster_node |
Source code
|
| load_expression_mat |
Source code
|
| load_genotype_mat |
Source code
|
| load_index_mat_list_to_cluster_node |
Source code
|
| load_index_mat_t_list_to_cluster_node |
Source code
|
| load_lambda1_list_to_cluster_node |
Source code
|
| load_mapping_data_to_cluster_node |
Source code
|
| load_mapping_shift_data_to_cluster_node |
Source code
|
| load_metaannotation_tbl |
Source code
|
| load_node_nr_to_cluster |
Source code
|
| load_takvf_list_to_cluster_node |
Source code
|
| load_theta_alphai_star_vect_to_cluster_node |
Source code
|
| load_theta_b_alphai_vect_from_cluster_node |
Source code
|
| makePSOCKcluster_or_environment |
Source code
|
| make_empty_list |
Source code
|
| my_caught_svd |
Source code
Source code
|
| my_cov |
Source code
|
| my_docall_rbind |
Source code
Source code
|
| my_scale |
Source code
|
| my_stop |
Source code
|
| my_tmpdir |
Source code
|
| mywhere |
Source code
|
| mywhere2 |
Source code
|
| paste_theta_b_alphai_vect_second |
Source code
|
| predict_directed_fast |
Source code
|
| prepare_D_mat |
Source code
|
| prepare_annotation_mapping_mat |
Source code
|
| prepare_data_per_chr |
Source code
|
| prepare_data_per_chr_not1KG |
Source code
|
| prepare_g_root_list |
Source code
|
| prepare_genotype_pcs_data |
Source code
|
| prepare_inputdata_lists |
Source code
|
| prepare_nonoptim_outl |
Source code
|
| prepare_observed_1KG_data |
Source code
|
| prepare_observed_data |
Source code
|
| prepare_theta_root_list |
Source code
|
| preprocess_gwas_summary_stat_tbl |
Source code
|
| present_in_all |
Source code
Source code
|
| process_Ls_on_node_list |
Source code
|
| process_Ls_on_node_wshift_list |
Source code
|
| process_gene_1KG |
Source code
|
| process_gene_not1KG |
Source code
|
| process_mapping_mats |
Source code
|
| process_upsilon |
Source code
|
| pull_out_dat |
Source code
|
| pull_out_dat_list_for_alphasplit |
Source code
|
| reassemble_Eu_b_list |
Source code
|
| reassemble_XtX |
Source code
|
| reduce_bagea_results |
Source code
|
| reformat_bagea_output2input |
Source code
|
| regress_out_pcs |
Source code
|
| regress_out_vects |
Source code
|
| remove_lowmaf_snps |
Source code
|
| rm_cluster |
Source code
|
| run_bagea |
Source code
|
| run_bagea_nonoptimized |
Source code
|
| run_calc_theta_b_omega_via_Eu_nu_on_node |
Source code
|
| run_cycle_across_allgenes_mpi_loc |
Source code
|
| run_cycle_across_allgenes_mpi_only_b_part |
Source code
|
| run_gene_cycle_lambda_b_nu |
Source code
|
| run_gene_cycle_only_alpha |
Source code
|
| run_gene_cycle_only_b |
Source code
|
| run_gene_cycle_wrapper |
Source code
|
| run_gene_cycle_wrapper_lambda_b_nu |
Source code
|
| run_gene_cycle_wrapper_only_b |
Source code
|
| run_globalE_list |
Source code
|
| scale_genotype_mat_1KG |
Source code
|
| set_all_theta_alphai_star_second |
Source code
|
| set_hyperparameter_list |
Source code
|
| setup_D_mat_with_checks |
Source code
|
| shift_mat_is_available |
Source code
|
| simple_sub_chi |
Source code
|
| simple_subsub_chi |
Source code
|
| simulate_params_from_hyperparams |
Source code
|
| simulate_y |
Source code
|
| simulate_z |
Source code
|
| source_on_nodes |
Source code
|
| split_along_length_lists |
Source code
|
| split_along_lengths |
Source code
|
| split_and_upload |
Source code
|
| split_gene_dat_list |
Source code
|
| subset_annotation_mat_cols |
Source code
|
| subset_annotation_mat_rows2chr |
Source code
|
| subset_annotation_mat_rows2range |
Source code
|
| subset_bagea_annotation_mat_onsnpnames |
Source code
|
| subset_expression_mat_chr |
Source code
|
| to_be_run_on_node_loc |
Source code
|
| to_be_run_on_node_only_b_part |
Source code
|
| update_Eu_ak |
Source code
|
| update_Eu_alphai |
Source code
|
| update_Eu_bj_Eu_lambdaj |
Source code
|
| update_Eu_chi2j |
Source code
|
| update_Eu_gammai_second_row_via_Eu_ak |
Source code
|
| update_Eu_gammai_second_row_via_Eu_ak_only_second_with_preindexi |
Source code
Source code
|
| update_Eu_kappai |
Source code
|
| update_Eu_lambda2 |
Source code
|
| update_Eu_nu_list |
Source code
|
| update_Eu_omega_list |
Source code
|
| update_Eu_tau2 |
Source code
|
| update_Eu_upsilon_list |
Source code
|
| update_hyperparameter_list |
Source code
|
| update_params |
Source code
|
| update_traces |
Source code
|
| upload_aux_data |
Source code
|
| upload_global_Elist |
Source code
|
| upload_index_mat |
Source code
|
| upload_lambda1 |
Source code
|
