├── .Rbuildignore ├── .github └── workflows │ └── jekyll-gh-pages.yml ├── .gitignore ├── CRAN-SUBMISSION ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── R_association_testing.R ├── Tables_graphs.R ├── combine_split.R ├── composite_phenotyping.R ├── concept_creation.R ├── data_field_phenotype_generation.R ├── data_filtering.R ├── data_preparation.R ├── extract_SNPs.R ├── formula_phenotype_generation.R ├── phecode_generating.R ├── phenotype_preparation.R ├── plink_association_testing.R └── primary_care_quant_phenotypes.R ├── README.md ├── _config.yml ├── cran-comments.md ├── inst └── extdata │ ├── GRS_PRS_template.csv.gz │ ├── PQP_codes │ ├── chloride_codes.txt.gz │ ├── potassium_codes.txt.gz │ └── sodium_codes.txt.gz │ ├── PheWAS_manifest.csv.gz │ ├── SNP_list_template.csv.gz │ ├── V2_concept_file_list.csv.gz │ ├── V2_drugs.csv.gz │ ├── clinical_concept_file_list.csv.gz │ ├── composite_phenotype_map.csv.gz │ ├── concept_codes │ ├── AECOPD_HES_other_primary_position_codes_rated.csv.gz │ ├── AECOPD_HES_primary_position_codes_rated.csv.gz │ ├── AECOPD_HES_secondary_position_codes_rated.csv.gz │ ├── AECOPD_primary_care_codes_rated.csv.gz │ ├── COPD_clinicalcodes_codes_rated.csv.gz │ ├── HIV_codes_rated.csv.gz │ ├── IBS_codes_rated.csv.gz │ ├── QTc_readcodes_codes_rated.csv.gz │ ├── acute_closed_angle_glaucoma_codes_rated.csv.gz │ ├── acute_kidney_injury_codes_rated.csv.gz │ ├── acute_urinary_retention_codes_rated.csv.gz │ ├── agranulocytosis_codes_rated.csv.gz │ ├── all_cancer_codes_rated.csv.gz │ ├── alpha1_antitrypsin_deficiency_codes_rated.csv.gz │ ├── alzheimers_codes_rated.csv.gz │ ├── amyotrophic_lateral_sclerosis_codes_rated.csv.gz │ ├── anaphylactic_reaction_codes_rated.csv.gz │ ├── antibiotics_COPD_drugs_BNF_DMD.csv.gz │ ├── antibiotics_COPD_drugs_V2_rated.csv.gz │ ├── aplastic_anaemia_codes_rated.csv.gz │ ├── asthma_codes_rated.csv.gz │ ├── bronchiectasis_codes_rated.csv.gz │ ├── carpal_tunnel_surgery_codes_rated.csv.gz │ ├── carpal_tunnel_syndrome_codes_rated.csv.gz │ ├── central_neuropathic_pain_codes_rated.csv.gz │ ├── cerebral_haemorrhage_codes_rated.csv.gz │ ├── depression_codes_rated.csv.gz │ ├── diabetes_all_codes_rated.csv.gz │ ├── diabetes_type_1_codes_rated.csv.gz │ ├── diabetes_type_2_codes_rated.csv.gz │ ├── diabetes_unclear_type_codes_rated.csv.gz │ ├── diabetic_neuropathy_codes_rated.csv.gz │ ├── diabetic_neuropathy_generic_codes_rated.csv.gz │ ├── emphysema_codes_rated.csv.gz │ ├── epilepsy_codes_rated.csv.gz │ ├── family_history_COPD_codes_rated.csv.gz │ ├── family_history_alzheimers_codes_rated.csv.gz │ ├── family_history_bowel_cancer_codes_rated.csv.gz │ ├── family_history_breast_cancer_codes_rated.csv.gz │ ├── family_history_diabetes_mellitus_codes_rated.csv.gz │ ├── family_history_heart_disease_codes_rated.csv.gz │ ├── family_history_hypertension_codes_rated.csv.gz │ ├── family_history_lung_cancer_codes_rated.csv.gz │ ├── family_history_parkinsons_codes_rated.csv.gz │ ├── family_history_prostate_cancer_codes_rated.csv.gz │ ├── family_history_severe_depression_codes_rated.csv.gz │ ├── family_history_stroke_codes_rated.csv.gz │ ├── gastrointestinal_bleed_codes_rated.csv.gz │ ├── haemarthrosis_codes_rated.csv.gz │ ├── haemothorax_codes_rated.csv.gz │ ├── headache_codes_rated.csv.gz │ ├── hearing_loss_codes_rated.csv.gz │ ├── herpes_codes_rated.csv.gz │ ├── huntingtons_codes_rated.csv.gz │ ├── leprosy_codes_rated.csv.gz │ ├── liver_failure_codes_rated.csv.gz │ ├── liver_failure_due_to_drugs_codes_rated.csv.gz │ ├── migraine_codes_rated.csv.gz │ ├── multiple_sclerosis_codes_rated.csv.gz │ ├── myocardial_infarction_codes_rated.csv.gz │ ├── non_IBS_codes_rated.csv.gz │ ├── other_dementia_codes_rated.csv.gz │ ├── parkinsons_codes_rated.csv.gz │ ├── parkinsons_drugs_BNF_DMD.csv.gz │ ├── parkinsons_drugs_V2_rated.csv.gz │ ├── prednisolone_COPD_drugs_BNF_DMD.csv.gz │ ├── prednisolone_COPD_drugs_V2_rated.csv.gz │ ├── rescue_pack_COPD_codes_rated.csv.gz │ ├── rhabdomyolysis_codes_rated.csv.gz │ ├── secondary_parkinsonism_codes_rated.csv.gz │ ├── seizure_codes_rated.csv.gz │ ├── sepsis_codes_rated.csv.gz │ ├── stevens_johnsons_syndrome_codes_rated.csv.gz │ ├── stroke_codes_rated.csv.gz │ ├── stroke_haemorrhagic_codes_rated.csv.gz │ ├── stroke_ischaemic_codes_rated.csv.gz │ ├── stroke_not_specified_codes_rated.csv.gz │ ├── sudden_cardiac_death_codes_rated.csv.gz │ ├── suicide_codes_rated.csv.gz │ ├── thyroid_eye_disease_codes_rated.csv.gz │ ├── tic_disorder_Read_codes.csv.gz │ ├── tinnitus_codes_rated.csv.gz │ ├── toxic_epidermal_necrolysis_codes_rated.csv.gz │ ├── transient_ischaemic_attack_codes_rated.csv.gz │ ├── unstable_angina_codes_rated.csv.gz │ └── ventricular_arrythmia_codes_rated.csv.gz │ ├── fields-minimum.txt.gz │ ├── genetic_file_guide.csv.gz │ ├── phecode_definitions.gz │ ├── phecode_map_rollup_ICD10.gz │ ├── phecode_map_rollup_ICD9.gz │ ├── prescription_concept_file_list.csv.gz │ ├── scripts │ ├── association_testing │ │ ├── 01_phenotype_preparation.R │ │ ├── 02_extracting_snps.R │ │ ├── 03a_PLINK_association_testing.R │ │ ├── 03b_R_association_testing.R │ │ ├── 04_combine_split.R │ │ └── 05_tables_graphs.R │ └── phenotype_generation │ │ ├── 01_minimum_data.R │ │ ├── 02_data_preparation.R │ │ ├── 03a_phecode_generation.R │ │ ├── 03b_data_field_phenotypes.R │ │ ├── 03c_creating_concepts.R │ │ ├── 03d_primary_care_quantitative_phenotypes.R │ │ ├── 04_formula_phenotypes.R │ │ └── 05_composite_phenotypes.R │ └── worked_example │ ├── CNV_example.gz │ ├── GPC.csv.gz │ ├── GRS_example_data.gz │ ├── GRS_guide │ ├── HES_Diag.csv.gz │ ├── KING_coef.csv.gz │ ├── PheWAS_ID_label_filter.gz │ ├── aoo_filter.txt.gz │ ├── death.csv.gz │ ├── death_date.csv.gz │ ├── example.bed │ ├── example.bim │ ├── example.fam.gz │ ├── example_manifest.gz │ ├── genetic_file_guide.csv │ ├── hesin.csv.gz │ ├── sex_filter.txt.gz │ ├── snp_info.gz │ └── ukb_data.csv.gz ├── man ├── AND.Rd ├── Deep_PheWAS_graphs_tables.Rd ├── GRS_association.Rd ├── GRS_association_testing.Rd ├── IVNT_transformation.Rd ├── NOT.Rd ├── R_association_function.Rd ├── R_association_testing.Rd ├── SR_data_out.Rd ├── adding_to_results.Rd ├── age_of_onset_pheno_creator.Rd ├── association_tests.Rd ├── calc_minus_source_ID.Rd ├── clinical_code_lookup.Rd ├── combine_split.Rd ├── combining_codes.Rd ├── combining_data_field.Rd ├── composite_phenotyping.Rd ├── concept_list_conversion.Rd ├── concept_source_data_extraction.Rd ├── converted_for_association.Rd ├── creating_concepts.Rd ├── curated_phenotype_creation.Rd ├── data_field_extraction.Rd ├── data_field_phenotyping.Rd ├── data_preparation_R.Rd ├── drug_code_lookup.Rd ├── exclusion_generator.Rd ├── fdr_calc.Rd ├── formula_phenotypes.Rd ├── generating_phecodes.Rd ├── graphs_tables_DeepPheWAS.Rd ├── group_id_creater.Rd ├── inner_names.Rd ├── join_cols_pheno.Rd ├── making_GRS_folders.Rd ├── making_case_lists.Rd ├── making_case_names.Rd ├── making_control_pop_lists.Rd ├── making_graphs.Rd ├── minimum_data_R.Rd ├── operator_list_conversion.Rd ├── per_group_function.Rd ├── per_group_none_GRS.Rd ├── per_group_per_trait_GRS.Rd ├── per_line_edit.Rd ├── per_pheno_ancestry.Rd ├── per_snp_function.Rd ├── phecoding.Rd ├── phenotype_preparation.Rd ├── plink_association_testing.Rd ├── plink_file_edit_join.Rd ├── primarycare_quantitative_phenotypes.Rd ├── quant_primary_care.Rd ├── recoding_variants.Rd ├── reducing_phenotypes.Rd ├── relate_remove_all_pops.Rd ├── relate_remove_fn.Rd ├── saving_files.Rd ├── saving_files_simple.Rd ├── selecting_phenotype_cases_N.Rd ├── setdiff_all.Rd ├── sex_specific_female.Rd ├── sex_specific_male.Rd ├── snp_extractor.Rd ├── snp_selection.Rd ├── spliting_by_population.Rd ├── sum_stats.Rd ├── summary_all_pops.Rd └── tab_data_clean.Rd └── tests ├── testthat.R └── testthat └── test-data_field_phenotype_generation.R /.Rbuildignore: 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