snipar package
Subpackages
- snipar.example package
- snipar.imputation package
- snipar.read package
- snipar.scripts package
- 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
Submodules
- snipar.config module
- snipar.correlate module
- snipar.errors module
- snipar.gtarray module
- snipar.gwas module
- snipar.ibd module
- snipar.ld module
- snipar.lmm module
- snipar.map module
- snipar.pedigree module
- 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
pgs
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
- snipar.preprocess module
- snipar.simulate module
am_indices()
compute_genetic_component()
compute_phenotype()
compute_phenotype_indirect()
compute_phenotype_vert()
compute_vcomps()
create_ped_output()
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
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_covar()
LinearMixedModel.fit_snps_eff()
LinearMixedModel.grad
LinearMixedModel.grid_search_reml()
LinearMixedModel.hessian
LinearMixedModel.logger
LinearMixedModel.reml_loglik
LinearMixedModel.scipy_optimize()
LinearMixedModel.sp_solve_dense3d()
LinearMixedModel.sp_solve_dense3d_lu()
LinearMixedModel.test_grad_hessian()
LinearMixedModel.varcomps
build_grm_arr()
build_ibdrel_arr()
build_sib_arr()
cached_property_depends_on()
match_grm_ids()
run_gcta_grm()
- snipar.utilities module