genal

• genal package
  • Submodules
  • genal.GENO module
    • GENO
      • GENO.name
      • GENO.data
      • GENO.data_clumped
      • GENO.phenotype
      • GENO.MR_data
      • GENO.ram
      • GENO.cpus
      • GENO.checks
      • GENO.reference_panel
      • GENO.clump()
      • GENO.prs()
      • GENO.set_phenotype()
      • GENO.association_test()
      • GENO.query_outcome()
      • GENO.MR()
      • GENO.MRpresso()
      • GENO.lift()
      • GENO.MR()
      • GENO.MRpresso()
      • GENO.association_test()
      • GENO.clump()
      • GENO.copy()
      • GENO.extract_snps()
      • GENO.get_reference_panel()
      • GENO.init_attributes()
      • GENO.name
      • GENO.outcome
      • GENO.data_clumped
      • GENO.cpus
      • GENO.ram
      • GENO.lift()
      • GENO.prs()
      • GENO.query_outcome()
      • GENO.save()
      • GENO.set_phenotype()
      • GENO.sort_group()
      • GENO.standardize()
  • genal.MR module
    • linreg()
    • mr_egger_regression()
    • mr_egger_regression_bootstrap()
    • mr_ivw()
    • mr_ivw_fe()
    • mr_ivw_re()
    • mr_pen_wm()
    • mr_sign()
    • mr_simple_median()
    • mr_uwr()
    • mr_weighted_median()
    • parallel_bootstrap_func()
    • weighted_median()
    • weighted_median_bootstrap()
  • genal.MR_tools module
    • MR_func()
    • apply_action_2()
    • check_required_columns()
    • flip_alleles()
    • harmonize_MR()
    • load_outcome_from_filepath()
    • load_outcome_from_geno_object()
    • mrpresso_func()
    • query_outcome_func()
  • genal.MRpresso module
    • getRSS_LOO()
    • getRandomData()
    • mr_presso()
    • parallel_RSS_LOO()
    • power_eigen()
  • genal.association module
    • association_test_func()
    • set_phenotype_func()
  • genal.clump module
    • clump_data()
  • genal.extract_prs module
    • create_bedlist()
    • extract_command_parallel()
    • extract_snps_from_combined_data()
    • extract_snps_func()
    • handle_multiallelic_variants()
    • merge_extracted_snps()
    • prepare_snp_list()
    • process_split_data()
    • prs_func()
    • report_snps_not_found()
    • setup_path()
  • genal.geno_tools module
    • Combine_GENO()
    • adjust_column_names()
    • check_allele_column()
    • check_arguments()
    • check_beta_column()
    • check_int_column()
    • check_p_column()
    • check_snp_column()
    • delete_tmp()
    • fill_coordinates_func()
    • fill_ea_nea()
    • fill_nea()
    • fill_se_p()
    • fill_snpids_func()
    • remove_na()
    • save_data()
  • genal.lift module
    • lift_coordinates()
    • lift_data()
    • lift_data_liftover()
    • post_lift_operations()
    • prepare_chain_file()
  • genal.proxy module
    • apply_proxies()
    • find_proxies()
    • query_outcome_proxy()
  • genal.tools module
    • check_bfiles()
    • default_config()
    • get_plink19_path()
    • get_reference_panel_path()
    • load_reference_panel()
    • read_config()
    • set_plink()
    • set_reference_folder()
    • write_config()
  • Module contents