--- a
+++ b/kgwas/params.py
@@ -0,0 +1,84 @@
+## The raw UKBB genotype data paths. If you have access to it, please modify the paths accordingly. 
+cohort_data_path = '/dfs/project/datasets/20220524-ukbiobank/data/cohort/'
+ukbb_data_path = '/dfs/project/datasets/20220524-ukbiobank/data/genetics/'
+main_data_path = '/dfs/project/datasets/20220524-ukbiobank/data/ukb_main/ukb52124.csv'
+kinship_path = '/dfs/project/datasets/20220524-ukbiobank/data/genetics/ukb_rel_a79791_s488170.dat'
+withdraw_path = '/dfs/project/datasets/20220524-ukbiobank/data/withdraw'
+fam_path = '/dfs/project/datasets/20220524-ukbiobank/data/genetics/ukb_lmdb_fam.csv'
+bim_path = '/dfs/project/datasets/20220524-ukbiobank/data/genetics/ukb_lmdb_bim.csv'
+
+scdrs_traits = ['UKB_460K.mental_NEUROTICISM',
+ 'PASS_FastingGlucose_Manning',
+ 'PASS_Lupus',
+ 'UKB_460K.biochemistry_HbA1c',
+ 'PASS_ADHD_Demontis2018',
+ 'UKB_460K.bmd_HEEL_TSCOREz',
+ 'UKB_460K.disease_HYPOTHYROIDISM_SELF_REP',
+ 'UKB_460K.blood_LYMPHOCYTE_COUNT',
+ 'PASS_Insomnia_Jansen2019',
+ 'UKB_460K.other_MORNINGPERSON',
+ 'UKB_460K.cov_SMOKING_STATUS',
+ 'UKB_460K.biochemistry_TotalBilirubin',
+ 'PASS_BIP_Stahl2019',
+ 'UKB_460K.biochemistry_HDLcholesterol',
+ 'PASS_UC_deLange2017',
+ 'UKB_460K.pigment_HAIR',
+ 'UKB_460K.body_HEIGHTz',
+ 'PASS_Worry_Nagel2018',
+ 'PASS_Type_2_Diabetes',
+ 'UKB_460K.body_BMIz',
+ 'UKB_460K.disease_HYPERTENSION_DIAGNOSED',
+ 'PASS_Primary_biliary_cirrhosis',
+ 'UKB_460K.blood_RED_COUNT',
+ 'UKB_460K.disease_CARDIOVASCULAR',
+ 'PASS_DrinksPerWeek_Liu2019',
+ 'PASS_SWB',
+ 'PASS_VerbalNumericReasoning_Davies2018',
+ 'UKB_460K.biochemistry_AlkalinePhosphatase',
+ 'UKB_460K.bp_DIASTOLICadjMEDz',
+ 'UKB_460K.disease_RESPIRATORY_ENT',
+ 'UKB_460K.biochemistry_Cholesterol',
+ 'PASS_Alzheimers_Jansen2019',
+ 'UKB_460K.repro_NumberChildrenEverBorn_Pooled',
+ 'UKB_460K.biochemistry_Triglycerides',
+ 'UKB_460K.body_BALDING1',
+ 'PASS_Coronary_Artery_Disease',
+ 'UKB_460K.blood_PLATELET_COUNT',
+ 'PASS_Multiple_sclerosis',
+ 'UKB_460K.disease_AID_ALL',
+ 'UKB_460K.repro_MENOPAUSE_AGE',
+ 'PASS_Type_1_Diabetes',
+ 'UKB_460K.lung_FVCzSMOKE',
+ 'UKB_460K.blood_EOSINOPHIL_COUNT',
+ 'UKB_460K.cancer_BREAST',
+ 'UKB_460K.repro_MENARCHE_AGE',
+ 'PASS_Intelligence_SavageJansen2018',
+ 'PASS_ReactionTime_Davies2018',
+ 'UKB_460K.biochemistry_SHBG',
+ 'UKB_460K.blood_WHITE_COUNT',
+ 'PASS_AtrialFibrillation_Nielsen2018',
+ 'UKB_460K.blood_MONOCYTE_COUNT',
+ 'UKB_460K.biochemistry_LDLdirect',
+ 'UKB_460K.biochemistry_TotalProtein',
+ 'UKB_460K.blood_MEAN_CORPUSCULAR_HEMOGLOBIN',
+ 'UKB_460K.cov_EDU_COLLEGE',
+ 'UKB_460K.body_WHRadjBMIz',
+ 'PASS_IBD_deLange2017',
+ 'PASS_SleepDuration_Dashti2019',
+ 'PASS_BIP_Mullins2021',
+ 'UKB_460K.cov_EDU_YEARS',
+ 'UKB_460K.bp_SYSTOLICadjMEDz',
+ 'UKB_460K.disease_ALLERGY_ECZEMA_DIAGNOSED',
+ 'UKB_460K.disease_ASTHMA_DIAGNOSED',
+ 'PASS_Schizophrenia_Pardinas2018',
+ 'PASS_Rheumatoid_Arthritis',
+ 'UKB_460K.lung_FEV1FVCzSMOKE',
+ 'PASS_Celiac',
+ 'UKB_460K.biochemistry_Glucose',
+ 'PASS_MDD_Howard2019',
+ 'PASS_GeneralRiskTolerance_KarlssonLinner2019',
+ 'PASS_CD_deLange2017',
+ 'UKB_460K.biochemistry_Testosterone_Male',
+ 'UKB_460K.blood_RBC_DISTRIB_WIDTH',
+ 'UKB_460K.impedance_BASAL_METABOLIC_RATEz',
+ 'UKB_460K.biochemistry_AlanineAminotransferase']
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