snipar package

Subpackages

• snipar.example package
  • Submodules
    • snipar.example.simulate_phenotype module
    • snipar.example.snipar_example_data module
      • load_example_data()
  • Module contents
• snipar.imputation package
  • Submodules
    • snipar.imputation.impute_from_sibs module
    • snipar.imputation.preprocess_data module
      • Classes
      • Functions
      • Person
      • add_control()
      • compute_aics()
      • estimate_f()
      • prepare_data()
      • prepare_gts()
      • preprocess_king()
      • recurcive_append()
  • Module contents
• snipar.read package
  • Submodules
    • snipar.read.bed module
      • get_gts_matrix_given_ped()
      • get_snps()
      • match_observed_and_imputed_snps()
      • read_PO_pairs_from_bed()
      • read_sibs_from_bed()
    • snipar.read.bgen module
      • get_gts_matrix_given_ped()
      • get_snps()
      • match_observed_and_imputed_snps()
      • read_PO_pairs_from_bgen()
      • read_sibs_from_bgen()
    • snipar.read.phenotype module
      • match_phenotype()
      • read_covariates()
      • read_phenotype()
  • Module contents
    • build_ped_from_par_gts()
    • get_gts_matrix()
    • get_ids_with_par()
    • get_ids_with_sibs()
    • get_ids_with_trios()
    • get_ids_with_trios_sibs()
• snipar.scripts package
  • Submodules
    • snipar.scripts.correlate module
      • main()
    • snipar.scripts.gts_matrix module
      • gts_matrix_chromosome()
      • main()
      • write_genoarray()
    • snipar.scripts.gwas module
      • main()
    • snipar.scripts.ibd module
      • main()
    • snipar.scripts.impute module
    • snipar.scripts.make_rdr_grms module
    • snipar.scripts.pgs module
      • main()
    • snipar.scripts.simulate module
      • main()
  • Module contents
• snipar.tests package
  • Submodules
    • snipar.tests.imputation_diagnostic module
    • snipar.tests.test_example module
    • snipar.tests.test_imputation module
    • snipar.tests.test_impute module
    • snipar.tests.test_impute_from_sibs module
    • snipar.tests.test_manhattan module
    • snipar.tests.test_pedigree_creation module
    • snipar.tests.test_sibreg module
    • snipar.tests.utils module
  • Module contents

Submodules

• snipar.config module
• snipar.correlate module
  • compute_corr()
  • estimate_cov()
  • estimate_cov_weights()
  • estimate_var()
  • estimate_weights()
  • jacknife()
  • jacknife_est()
  • read_sumstats_file()
  • read_sumstats_files()
  • reweighted_estimate_cov()
  • reweighted_estimate_var()
  • sumstats
    • sumstats.compute_ld_scores()
    • sumstats.concatenate()
    • sumstats.cor_direct_avg_NTC()
    • sumstats.cor_direct_pop()
    • sumstats.filter()
    • sumstats.filter_NAs()
    • sumstats.filter_corrs()
    • sumstats.filter_maf()
    • sumstats.scores_from_ldsc()
• snipar.docgen module
  • get_parser_doc()
• snipar.errors module
  • count_ME()
  • estimate_genotyping_error_rate()
  • g_error
    • g_error.bayes_shrink()
  • mendelian_errors()
• snipar.gtarray module
  • gtarray
    • gtarray.add()
    • gtarray.compute_freqs()
    • gtarray.compute_info()
    • gtarray.diagonalise()
    • gtarray.fill_NAs()
    • gtarray.filter()
    • gtarray.filter_ids()
    • gtarray.filter_info()
    • gtarray.filter_maf()
    • gtarray.filter_missingness()
    • gtarray.mean_normalise()
    • gtarray.scale()
  • impute_missing()
  • impute_unrel_par_gts()
• snipar.gwas module
  • compute_batch_boundaries()
  • find_common_ind_ids()
  • outarray_effect()
  • process_batch()
  • process_chromosome()
  • split_batches()
  • write_output()
  • write_txt_output()
• snipar.ibd module
  • find_segments()
  • infer_ibd()
  • infer_ibd_chr()
  • make_dynamic()
  • p_ibd_0()
  • p_ibd_1()
  • p_ibd_2()
  • p_obs_given_IBD()
  • segment
    • segment.to_text()
  • smooth_ibd()
  • smooth_segments()
  • transition_matrix()
  • viterbi()
  • write_segs()
  • write_segs_from_matrix()
• snipar.ld module
  • compute_ld_scores()
  • ldscores_from_bed()
  • r2_est()
• snipar.map module
  • decode_map_from_pos()
  • get_map_positions()
  • map_from_bed()
  • pos_to_cM()
• snipar.numrange module
  • NumRangeAction
  • parseNumRange()
• snipar.pedigree module
  • Person
  • create_pedigree()
  • find_individuals_with_sibs()
  • get_sibpairs_from_king()
  • get_sibpairs_from_ped()
• snipar.pgs module
  • am_adj_2gen()
  • am_adj_2gen_calc()
  • compute()
  • fit_pgs_model()
  • h2f_parse()
  • make_and_fit_model()
  • make_grms()
  • npg_am_adj()
  • opg_am_adj()
  • pgarray
    • pgarray.add()
    • pgarray.am_adj()
    • pgarray.compute_grandpar()
    • pgarray.estimate_r()
    • pgarray.filter_bpg()
    • pgarray.scale()
    • pgarray.write()
  • pgs
    • pgs.compute()
    • pgs.remove_zeros()
  • pgs_cor_lik()
  • pgs_corr_likelihood()
  • pgs_corr_likelihood_fam()
  • pgs_corr_matrix()
  • read_pgs()
  • read_weights()
  • simulate_r_inf()
  • write_2gen_adj_ests()
  • write_estimates()
• snipar.pgs_am module
  • alpha_from_alpha()
  • alpha_from_beta()
  • check_se_calc()
  • delta_method()
  • estimate_h2eq()
  • estimate_k()
  • estimate_r()
  • estimate_rho()
  • h2eq_se()
  • k_se()
  • r_se()
  • rho_se()
  • se_alpha_from_alpha()
  • se_alpha_from_beta()
  • se_check()
  • se_v_eta_delta()
  • simulate_ests()
  • simulation_check()
  • v_eta_delta()
• snipar.preprocess module
  • find_gts()
  • find_par_gts()
  • get_fam_means()
  • get_indices_given_ped()
  • get_indices_given_ped_sibs()
  • get_indices_given_ped_trios()
  • get_indices_given_ped_trios_sibs()
  • make_gts_matrix()
  • make_num_obs_par_al_matrix()
  • remove_sibs()
• snipar.simulate module
  • am_indices()
  • compute_genetic_component()
  • compute_phenotype()
  • compute_phenotype_indirect()
  • compute_phenotype_vert()
  • compute_vcomps()
  • create_ped_output()
  • find_sibs_and_cousins()
  • forward_sim()
  • haps_from_bgen()
  • impute_all_fams()
  • impute_all_fams_phased()
  • impute_from_sibs()
  • impute_from_sibs_phased()
  • meiosis()
  • produce_next_gen()
  • produce_next_gen_unlinked()
  • random_mating_indices()
  • simulate_effects()
  • simulate_first_gen()
  • simulate_freqs()
  • simulate_haplotypes()
  • simulate_recombinations()
• snipar.slmm module
  • GradHessComponents
    • GradHessComponents.P_varcomp_mats
    • GradHessComponents.P_y
  • LinearMixedModel
    • LinearMixedModel.P_attrs
    • LinearMixedModel.V
    • LinearMixedModel.V_logdet
    • LinearMixedModel.V_lu
    • LinearMixedModel.Vinv_Z
    • LinearMixedModel.Vinv_e
    • LinearMixedModel.Vinv_mat()
    • LinearMixedModel.Vinv_varcomp_mats
    • LinearMixedModel.Vinv_y
    • LinearMixedModel.ai_reml()
    • LinearMixedModel.dense_reml_loglik()
    • LinearMixedModel.fit_snps_eff()
    • LinearMixedModel.grad
    • LinearMixedModel.grid_search_reml()
    • LinearMixedModel.hessian
    • LinearMixedModel.reml_loglik
    • LinearMixedModel.robust_est()
    • LinearMixedModel.scipy_optimize()
    • LinearMixedModel.sib_diff_est()
    • LinearMixedModel.sp_mul_dense3d()
    • LinearMixedModel.sp_solve_dense3d()
    • LinearMixedModel.sp_solve_dense3d_lu()
    • LinearMixedModel.trios_sibs_est()
    • LinearMixedModel.varcomps
  • build_grm_arr()
  • build_ibdrel_arr()
  • build_sib_arr()
  • cached_property_depends_on()
  • match_grm_ids()
• snipar.types module
• snipar.utilities module
  • convert_str_array()
  • coord2linear()
  • encode_str_array()
  • get_parser_doc()
  • linear2coord()
  • make_id_dict()
  • open_bgen()
  • outfile_name()
  • parse_filelist()
  • parse_obsfiles()
  • read_bgen()

Module contents