Index

_

__init__() (karyohmm.io.DataReader method) (karyohmm.karyohmm.AneuploidyHMM method) (karyohmm.karyohmm.MccEst method) (karyohmm.karyohmm.MetaHMM method) (karyohmm.karyohmm.MosaicEst method) (karyohmm.karyohmm.PhaseCorrect method) (karyohmm.karyohmm.PocHMM method) (karyohmm.karyohmm.QuadHMM method) (karyohmm.karyohmm.RecombEst method) (karyohmm.simulator.PGTSim method) (karyohmm.simulator.PGTSimBase method) (karyohmm.simulator.PGTSimMosaic method) (karyohmm.simulator.PGTSimSegmental method) (karyohmm.simulator.PGTSimVCF method)

A

add_baf() (karyohmm.karyohmm.PhaseCorrect method) add_true_haps() (karyohmm.karyohmm.PhaseCorrect method)

AneuploidyHMM (class in karyohmm.karyohmm) aploid (karyohmm.karyohmm.AneuploidyHMM attribute) (karyohmm.karyohmm.MetaHMM attribute)

B

backward_algorithm() (karyohmm.karyohmm.MetaHMM method) (karyohmm.karyohmm.PocHMM method) (karyohmm.karyohmm.QuadHMM method)

C

ci_mle_cf() (karyohmm.karyohmm.MosaicEst method) correct_haps_viterbi() (karyohmm.karyohmm.PhaseCorrect method) create_genotyping_errors() (karyohmm.simulator.PGTSimBase method)

create_switch_errors() (karyohmm.simulator.PGTSimBase method) create_switch_errors_help() (karyohmm.simulator.PGTSimBase method) create_transition_matrix() (karyohmm.karyohmm.MosaicEst method)

D

DataReader (class in karyohmm.io)

det_recomb_sex() (karyohmm.karyohmm.QuadHMM method) draw_parental_genotypes() (karyohmm.simulator.PGTSimBase method)

E

est_mcc_genome_phased_poc() (karyohmm.karyohmm.MccEst method) est_mcc_genome_phased_trio() (karyohmm.karyohmm.MccEst method) est_mcc_genome_poc() (karyohmm.karyohmm.MccEst method) est_mcc_genome_trio() (karyohmm.karyohmm.MccEst method) est_mcc_per_chrom_phased_poc() (karyohmm.karyohmm.MccEst method) est_mcc_per_chrom_phased_trio() (karyohmm.karyohmm.MccEst method) est_mcc_per_chrom_poc() (karyohmm.karyohmm.MccEst method) est_mcc_per_chrom_trio() (karyohmm.karyohmm.MccEst method) est_mcc_phased_poc() (karyohmm.karyohmm.MccEst method)

est_mcc_phased_trio() (karyohmm.karyohmm.MccEst method) est_mcc_poc() (karyohmm.karyohmm.MccEst method) est_mcc_trio() (karyohmm.karyohmm.MccEst method) est_mle_cf() (karyohmm.karyohmm.MosaicEst method) est_sharing() (karyohmm.karyohmm.QuadHMM method) est_sigma_pi0() (karyohmm.karyohmm.AneuploidyHMM method) (karyohmm.karyohmm.PocHMM method) est_sigma_pi0s() (karyohmm.karyohmm.PhaseCorrect method) estimate_crossovers() (karyohmm.karyohmm.RecombEst method) estimate_switch_err_true() (karyohmm.karyohmm.PhaseCorrect method)

F

finalize_recomb_events() (karyohmm.karyohmm.RecombEst method) flag_parental_genotype_errors() (karyohmm.karyohmm.MetaHMM method) (karyohmm.karyohmm.PhaseCorrect method) (karyohmm.karyohmm.QuadHMM method) forward_algo_full() (karyohmm.karyohmm.MosaicEst method) forward_algorithm() (karyohmm.karyohmm.MetaHMM method) (karyohmm.karyohmm.PocHMM method) (karyohmm.karyohmm.QuadHMM method)

forward_backward() (karyohmm.karyohmm.MetaHMM method) (karyohmm.karyohmm.PocHMM method) (karyohmm.karyohmm.QuadHMM method) full_param_inference() (karyohmm.karyohmm.AneuploidyHMM method) full_ploidy_sim() (karyohmm.simulator.PGTSim method) full_segmental_sim() (karyohmm.simulator.PGTSimSegmental method)

G

gen_parental_haplotypes() (karyohmm.simulator.PGTSimVCF method) genotype_embryo() (karyohmm.karyohmm.MetaHMM method)

genotype_parent() (karyohmm.karyohmm.PocHMM method) get_state_str() (karyohmm.karyohmm.AneuploidyHMM method)

I

identify_switch_intervals() (karyohmm.karyohmm.RecombEst method) infer_missing_af() (karyohmm.karyohmm.PocHMM method) infer_origin() (karyohmm.karyohmm.MosaicEst method)

informative_markers() (karyohmm.karyohmm.RecombEst method) isolate_recomb() (karyohmm.karyohmm.QuadHMM method) isolate_recomb_events() (karyohmm.karyohmm.RecombEst method)

K

karyohmm.io module

karyotypes (karyohmm.karyohmm.MetaHMM attribute) (karyohmm.karyohmm.QuadHMM attribute)

L

loglik_mcc_genome_phased_poc() (karyohmm.karyohmm.MccEst method) loglik_mcc_genome_phased_trio() (karyohmm.karyohmm.MccEst method) loglik_mcc_genome_poc() (karyohmm.karyohmm.MccEst method) loglik_mcc_genome_trio() (karyohmm.karyohmm.MccEst method)

loglik_mcc_phased_poc() (karyohmm.karyohmm.MccEst method) loglik_mcc_phased_trio() (karyohmm.karyohmm.MccEst method) loglik_mcc_poc() (karyohmm.karyohmm.MccEst method) loglik_mcc_trio() (karyohmm.karyohmm.MccEst method) lrt_cf() (karyohmm.karyohmm.MosaicEst method)

M

map_path() (karyohmm.karyohmm.QuadHMM method) marginal_posterior_karyotypes() (karyohmm.karyohmm.MetaHMM method) mcc_ci_phased_poc() (karyohmm.karyohmm.MccEst method) mcc_ci_phased_trio() (karyohmm.karyohmm.MccEst method) mcc_ci_poc() (karyohmm.karyohmm.MccEst method) mcc_ci_trio() (karyohmm.karyohmm.MccEst method)

MccEst (class in karyohmm.karyohmm) MetaHMM (class in karyohmm.karyohmm) mixed_ploidy_sim() (karyohmm.simulator.PGTSimMosaic method) module karyohmm.io MosaicEst (class in karyohmm.karyohmm)

P

PGTSim (class in karyohmm.simulator) PGTSimBase (class in karyohmm.simulator) PGTSimMosaic (class in karyohmm.simulator) PGTSimSegmental (class in karyohmm.simulator)

PGTSimVCF (class in karyohmm.simulator) PhaseCorrect (class in karyohmm.karyohmm) ploidy (karyohmm.karyohmm.AneuploidyHMM attribute) PocHMM (class in karyohmm.karyohmm) posterior_karyotypes() (karyohmm.karyohmm.MetaHMM method)

Q

QuadHMM (class in karyohmm.karyohmm)

R

read_data() (karyohmm.io.DataReader method) read_data_df() (karyohmm.io.DataReader method) read_data_np() (karyohmm.io.DataReader method)

RecombEst (class in karyohmm.karyohmm) refine_recomb_events() (karyohmm.karyohmm.RecombEst method) restrict_path() (karyohmm.karyohmm.QuadHMM method) restrict_states() (karyohmm.karyohmm.QuadHMM method)

S

second_refine_recomb() (karyohmm.karyohmm.RecombEst method) seg_aneuploidy() (karyohmm.simulator.PGTSimSegmental method) sibling_euploid_sim() (karyohmm.simulator.PGTSim method) sim_b_allele_freq() (karyohmm.simulator.PGTSimBase method) sim_b_allele_freq_segmental() (karyohmm.simulator.PGTSimSegmental method) sim_cell_contamination() (karyohmm.simulator.PGTSim method) sim_from_haps() (karyohmm.simulator.PGTSim method) (karyohmm.simulator.PGTSimMosaic method) (karyohmm.simulator.PGTSimSegmental method) sim_haplotype_paths() (karyohmm.simulator.PGTSimBase method)

sim_haplotype_paths_segmental() (karyohmm.simulator.PGTSimSegmental method) sim_haplotype_paths_upd() (karyohmm.simulator.PGTSimBase method) sim_haplotype_ref_panel() (karyohmm.simulator.PGTSimBase method) sim_joint_het() (karyohmm.simulator.PGTSimBase method) sim_logR_ratio() (karyohmm.simulator.PGTSimBase method) sim_read_counts() (karyohmm.simulator.PGTSimBase method) sim_read_counts_segmental() (karyohmm.simulator.PGTSimSegmental method) STATE_NAMES (karyohmm.karyohmm.MosaicEst attribute) states (karyohmm.karyohmm.MetaHMM attribute) (karyohmm.karyohmm.QuadHMM attribute)

V

viterbi_algorithm() (karyohmm.karyohmm.MetaHMM method) (karyohmm.karyohmm.QuadHMM method)

viterbi_path() (karyohmm.karyohmm.QuadHMM method) viterbi_phase_correct() (karyohmm.karyohmm.PhaseCorrect method)