snipar.simulate module

snipar.simulate.am_indices(yp, ym, r)

snipar.simulate.compute_genetic_component(haps, causal, a)

snipar.simulate.compute_phenotype(haps, causal, a, sigma2)

snipar.simulate.compute_phenotype_indirect(haps, old_haps, father_indices, mother_indices, causal, a, b, sigma2)

snipar.simulate.compute_phenotype_vert(haps, causal, a, sigma2, beta_vert, Y_p, Y_m)

snipar.simulate.compute_vcomps(G_p, G_m, Y_p, Y_m, delta_p=None, delta_m=None, v_indirect=0, eta_p=None, eta_m=None, verbose=True)

snipar.simulate.create_ped_output(G_males, G_females, Y_males, Y_females, Y_p, Y_m, delta_p, delta_m, eta_males=None, eta_females=None, eta_p=None, eta_m=None, father_indices=None, mother_indices=None, gen=None, header=True)

snipar.simulate.forward_sim(haps, maps, ngen_random, ngen_am, unlinked, n_causal, h2, v_indirect=0, r_direct_indirect=0, beta_vert=0, r_y=None)

snipar.simulate.haps_from_bgen(bgenfiles, chr_range)

snipar.simulate.impute_all_fams(gts, freqs, ibd)

snipar.simulate.impute_all_fams_phased(haps, freqs, ibd)

snipar.simulate.impute_from_sibs(g1, g2, ibd, f)

snipar.simulate.impute_from_sibs_phased(g1, g2, ibd, f)

snipar.simulate.meiosis(map, n=1)

snipar.simulate.produce_next_gen(father_indices, mother_indices, males, females, map)

snipar.simulate.produce_next_gen_unlinked(father_indices, mother_indices, males, females)

snipar.simulate.random_mating_indices(nfam)

snipar.simulate.simulate_effects(haps, n_causal, h2, old_haps=None, v_indirect=0, r_direct_indirect=0, father_indices=None, mother_indices=None)

snipar.simulate.simulate_first_gen(nfam, ncausal, maf=None, min_maf=0.05)

snipar.simulate.simulate_freqs(nsnp, maf=None, min_maf=None, Fst=0)

snipar.simulate.simulate_haplotypes(freqs, nfam)

snipar.simulate.simulate_recombinations(map)