initialize ukbb
Examples
ukbb <- ukbb_init()
names(ukbb)
#> [1] "AC_CUTOFFS"
#> [2] "AF_CUTOFFS"
#> [3] "CHROMOSOMES"
#> [4] "ENGLAND_RECRUITMENT_CENTERS"
#> [5] "MIN_CASES"
#> [6] "MIN_CASES_ALL"
#> [7] "MIN_CASES_EUR"
#> [8] "MISSENSE_CSQS"
#> [9] "NULL_STR"
#> [10] "NULL_STR_KEY"
#> [11] "OTHER_CSQS"
#> [12] "PHENO_COLUMN_FIELDS"
#> [13] "PHENO_DESCRIPTION_FIELDS"
#> [14] "PHENO_GWAS_FIELDS"
#> [15] "PHENO_KEY_FIELDS"
#> [16] "PILOT_PHENOTYPES"
#> [17] "PLOF_CSQS"
#> [18] "POPS"
#> [19] "P_THRESHOLDS"
#> [20] "REFERENCE_GENOME"
#> [21] "SIG_THRESHOLD"
#> [22] "SYNONYMOUS_CSQS"
#> [23] "UKB_GNOMAD_POP_MAPPING"
#> [24] "add_coding_information"
#> [25] "add_white_noise_pheno"
#> [26] "add_whr"
#> [27] "all_axis_join"
#> [28] "annotate_nearest_gene"
#> [29] "annotation_case_builder"
#> [30] "annotation_case_builder_ukb_legacy"
#> [31] "annotations"
#> [32] "brain_mri_data_path"
#> [33] "bucket"
#> [34] "check_timing_type"
#> [35] "check_trait_types"
#> [36] "coding_ht_path"
#> [37] "combine_datasets"
#> [38] "combine_pheno_files"
#> [39] "combine_pheno_files_multi_sex"
#> [40] "combine_pheno_files_multi_sex_legacy"
#> [41] "combine_phenotypes"
#> [42] "combine_phenotypes_in_mt"
#> [43] "combine_phenotypes_with_name"
#> [44] "compute_cases_binary"
#> [45] "compute_n_cases"
#> [46] "conditional_phenotypes"
#> [47] "create_broadcast_dict"
#> [48] "create_gene_map_ht"
#> [49] "create_genome_intervals_file"
#> [50] "csv"
#> [51] "downsample_table_by_x_y"
#> [52] "explode_by_p_threshold"
#> [53] "explode_lambda_ht"
#> [54] "filter_and_annotate_ukb_data"
#> [55] "filter_ht_for_plink"
#> [56] "filter_lambda_gc"
#> [57] "first_exposure_and_activity_monitor_data_path"
#> [58] "format_entries"
#> [59] "format_pheno_dir"
#> [60] "generate_lambda_ht_by_freq"
#> [61] "generate_qc_lambda_aggregator"
#> [62] "generic"
#> [63] "genotype_bm_path"
#> [64] "genotype_loading"
#> [65] "genotype_samples_ht_path"
#> [66] "genotypes"
#> [67] "get_age_sex_tsv_path"
#> [68] "get_all_codings"
#> [69] "get_analysis_data_path"
#> [70] "get_biomarker_ht_path"
#> [71] "get_cases_and_controls_from_log"
#> [72] "get_clump_sumstats_bm_path"
#> [73] "get_clump_sumstats_col_ht_path"
#> [74] "get_clumping_results_path"
#> [75] "get_coding_path"
#> [76] "get_codings"
#> [77] "get_covariates"
#> [78] "get_covariates_ht_path"
#> [79] "get_covid_data_path"
#> [80] "get_custom_pheno_path"
#> [81] "get_death_data_path"
#> [82] "get_files_in_parent_directory"
#> [83] "get_filtered_mt"
#> [84] "get_filtered_mt_with_x"
#> [85] "get_final_lambdas_path"
#> [86] "get_final_sample_set"
#> [87] "get_full_icd_data_description"
#> [88] "get_gene_intervals_path"
#> [89] "get_gp_data_tsv_path"
#> [90] "get_gwas_sig_path"
#> [91] "get_heritability_dict"
#> [92] "get_heritability_from_log"
#> [93] "get_heritability_txt_path"
#> [94] "get_hesin_data_path"
#> [95] "get_hesin_delivery_ht_path"
#> [96] "get_hesin_mt_path"
#> [97] "get_hesin_raw_data_path"
#> [98] "get_hm3_snplist_path"
#> [99] "get_hq_samples"
#> [100] "get_inverse_normalize_status"
#> [101] "get_ld_matrix_path"
#> [102] "get_ld_score_flat_file_path"
#> [103] "get_ld_score_ht_path"
#> [104] "get_ld_variant_index_path"
#> [105] "get_meta_analysis_results_path"
#> [106] "get_missing_codings"
#> [107] "get_modified_key"
#> [108] "get_n_even_intervals"
#> [109] "get_null_model_timing"
#> [110] "get_pheno_dict"
#> [111] "get_pheno_manifest_path"
#> [112] "get_pheno_output_path"
#> [113] "get_phenos_to_run"
#> [114] "get_phenotype_results_qc_path"
#> [115] "get_phenotype_summary_path"
#> [116] "get_phesant_all_phenos_tsv_path"
#> [117] "get_phesant_reassignments"
#> [118] "get_prs_assess_ht_path"
#> [119] "get_prs_bm_path"
#> [120] "get_prs_mt_path"
#> [121] "get_pruned_tsv_path"
#> [122] "get_results_prefix"
#> [123] "get_results_timing_ht_path"
#> [124] "get_results_timing_tsv_path"
#> [125] "get_saige_timing_grep"
#> [126] "get_saige_version_from_log"
#> [127] "get_sample_file"
#> [128] "get_top_p_from_mt"
#> [129] "get_top_p_path"
#> [130] "get_ukb_additional_phenos_description_path"
#> [131] "get_ukb_additional_phenos_tsv_path"
#> [132] "get_ukb_af_ht_path"
#> [133] "get_ukb_grm_mt_path"
#> [134] "get_ukb_grm_plink_path"
#> [135] "get_ukb_grm_pruned_ht_path"
#> [136] "get_ukb_imputed_data"
#> [137] "get_ukb_meta"
#> [138] "get_ukb_meta_pop_tsv_path"
#> [139] "get_ukb_pheno_ht_path"
#> [140] "get_ukb_pheno_mt"
#> [141] "get_ukb_pheno_mt_path"
#> [142] "get_ukb_phesant_summary_tsv_path"
#> [143] "get_ukb_samples_file_path"
#> [144] "get_ukb_sumstats_biomarkers_mt_path"
#> [145] "get_ukb_sumstats_mt_path"
#> [146] "get_ukb_vep_path"
#> [147] "get_variant_results_path"
#> [148] "get_variant_results_qc_path"
#> [149] "get_vep_formatted_data"
#> [150] "hl"
#> [151] "icd9_codings_ht_path"
#> [152] "icd9_codings_tsv_path"
#> [153] "icd_codings_ht_path"
#> [154] "icd_codings_tsv_path"
#> [155] "irnt"
#> [156] "join_pheno_hts_to_mt"
#> [157] "ld"
#> [158] "load_activity_monitor_data"
#> [159] "load_all_mfi_data"
#> [160] "load_brain_mri_data"
#> [161] "load_covid_data"
#> [162] "load_custom_pheno"
#> [163] "load_dob_ht"
#> [164] "load_final_sumstats_mt"
#> [165] "load_first_occurrence_data"
#> [166] "load_gene_data"
#> [167] "load_hesin_data"
#> [168] "load_icd_data"
#> [169] "load_prescription_data"
#> [170] "load_showcase"
#> [171] "load_variant_data"
#> [172] "locus_alleles_to_chr_pos_ref_alt"
#> [173] "mac_category_case_builder"
#> [174] "make_pairwise_ht"
#> [175] "mwzj_hts_by_tree"
#> [176] "os"
#> [177] "pairwise_cooccurrence_ht_path"
#> [178] "pairwise_correlation_ht_path"
#> [179] "pheno_description_path"
#> [180] "pheno_description_raw_path"
#> [181] "pheno_folder"
#> [182] "pheno_ht_to_mt"
#> [183] "phenotype_loading"
#> [184] "phenotype_munging"
#> [185] "phenotypes"
#> [186] "phesant_biomarker_phenotypes_tsv_path"
#> [187] "phesant_folder"
#> [188] "post_process_gene_map_ht"
#> [189] "pre_phesant_biomarkers_tsv_path"
#> [190] "pre_phesant_tsv_path"
#> [191] "pre_process_data_dictionary"
#> [192] "prescription_mapping_path"
#> [193] "prescription_tsv_path"
#> [194] "public_bucket"
#> [195] "public_bucket_free"
#> [196] "pull_out_col_keys"
#> [197] "pull_out_fields_from_entries"
#> [198] "re"
#> [199] "recode_pkd_to_legacy"
#> [200] "recode_pkd_to_new"
#> [201] "recode_single_pkd_to_legacy"
#> [202] "recode_single_pkd_to_new"
#> [203] "resources"
#> [204] "results"
#> [205] "results_loading"
#> [206] "separate_results_mt_by_pop"
#> [207] "stringify_pheno_key_dict"
#> [208] "subprocess"
#> [209] "summarize_data"
#> [210] "temp_bucket"
#> [211] "temp_bucket_7day"
#> [212] "tempfile"
#> [213] "ukb_imputed_bgen_path"
#> [214] "ukb_imputed_info_ht_path"
#> [215] "ukb_imputed_info_path"
#> [216] "unify_saige_burden_ht_schema"
#> [217] "unify_saige_ht_schema"
#> [218] "unify_saige_ht_variant_schema"
#> [219] "union_ht"
#> [220] "union_hts_by_tree"
#> [221] "union_mts_by_tree"
#> [222] "utils"
#> [223] "uuid"