Welcome to karyohmm’s documentation!

Karyohmm is an HMM-based model for aneuploidy detection in PGT-A datasets.

Karyohmm implements methods for haplotype based analyses of copy number changes, crossover recombination, and phasing from array intensity data when parental genotypes are available.

Implementation of read-based methods to support NGS-based PGT-A is a work in progress.

Contents:

• karyohmm API Reference
  • Core HMM Models
    • MetaHMM
      • MetaHMM.states
      • MetaHMM.karyotypes
      • MetaHMM.aploid
      • MetaHMM.__init__()
      • MetaHMM.forward_algorithm()
      • MetaHMM.backward_algorithm()
      • MetaHMM.forward_backward()
      • MetaHMM.viterbi_algorithm()
      • MetaHMM.marginal_posterior_karyotypes()
      • MetaHMM.posterior_karyotypes()
      • MetaHMM.genotype_embryo()
      • MetaHMM.flag_parental_genotype_errors()
    • QuadHMM
      • QuadHMM.states
      • QuadHMM.karyotypes
      • QuadHMM.__init__()
      • QuadHMM.forward_algorithm()
      • QuadHMM.backward_algorithm()
      • QuadHMM.forward_backward()
      • QuadHMM.viterbi_algorithm()
      • QuadHMM.restrict_path()
      • QuadHMM.restrict_states()
      • QuadHMM.viterbi_path()
      • QuadHMM.map_path()
      • QuadHMM.flag_parental_genotype_errors()
      • QuadHMM.det_recomb_sex()
      • QuadHMM.isolate_recomb()
      • QuadHMM.est_sharing()
    • PocHMM
      • PocHMM.__init__()
      • PocHMM.est_sigma_pi0()
      • PocHMM.forward_algorithm()
      • PocHMM.backward_algorithm()
      • PocHMM.forward_backward()
      • PocHMM.genotype_parent()
      • PocHMM.infer_missing_af()
  • Mosaic and Contamination Estimators
    • MosaicEst
      • MosaicEst.STATE_NAMES
      • MosaicEst.__init__()
      • MosaicEst.create_transition_matrix()
      • MosaicEst.forward_algo_full()
      • MosaicEst.est_mle_cf()
      • MosaicEst.ci_mle_cf()
      • MosaicEst.lrt_cf()
      • MosaicEst.infer_origin()
    • MccEst
      • MccEst.__init__()
      • MccEst.loglik_mcc_poc()
      • MccEst.loglik_mcc_trio()
      • MccEst.est_mcc_poc()
      • MccEst.est_mcc_trio()
      • MccEst.mcc_ci_poc()
      • MccEst.mcc_ci_trio()
      • MccEst.loglik_mcc_phased_trio()
      • MccEst.loglik_mcc_phased_poc()
      • MccEst.est_mcc_phased_trio()
      • MccEst.est_mcc_phased_poc()
      • MccEst.mcc_ci_phased_trio()
      • MccEst.mcc_ci_phased_poc()
      • MccEst.loglik_mcc_genome_poc()
      • MccEst.loglik_mcc_genome_trio()
      • MccEst.loglik_mcc_genome_phased_poc()
      • MccEst.loglik_mcc_genome_phased_trio()
      • MccEst.est_mcc_genome_poc()
      • MccEst.est_mcc_genome_trio()
      • MccEst.est_mcc_genome_phased_poc()
      • MccEst.est_mcc_genome_phased_trio()
      • MccEst.est_mcc_per_chrom_poc()
      • MccEst.est_mcc_per_chrom_trio()
      • MccEst.est_mcc_per_chrom_phased_poc()
      • MccEst.est_mcc_per_chrom_phased_trio()
  • Recombination and Phase Correction
    • RecombEst
      • RecombEst.__init__()
      • RecombEst.informative_markers()
      • RecombEst.refine_recomb_events()
      • RecombEst.isolate_recomb_events()
      • RecombEst.identify_switch_intervals()
      • RecombEst.second_refine_recomb()
      • RecombEst.finalize_recomb_events()
      • RecombEst.estimate_crossovers()
    • PhaseCorrect
      • PhaseCorrect.__init__()
      • PhaseCorrect.add_true_haps()
      • PhaseCorrect.add_baf()
      • PhaseCorrect.est_sigma_pi0s()
      • PhaseCorrect.correct_haps_viterbi()
      • PhaseCorrect.viterbi_phase_correct()
      • PhaseCorrect.flag_parental_genotype_errors()
      • PhaseCorrect.estimate_switch_err_true()
  • Base Class
    • AneuploidyHMM
      • AneuploidyHMM.ploidy
      • AneuploidyHMM.aploid
      • AneuploidyHMM.__init__()
      • AneuploidyHMM.get_state_str()
      • AneuploidyHMM.est_sigma_pi0()
      • AneuploidyHMM.full_param_inference()
  • Simulators
    • PGTSim
      • PGTSim.__init__()
      • PGTSim.full_ploidy_sim()
      • PGTSim.sibling_euploid_sim()
      • PGTSim.sim_from_haps()
      • PGTSim.sim_cell_contamination()
    • PGTSimMosaic
      • PGTSimMosaic.__init__()
      • PGTSimMosaic.mixed_ploidy_sim()
      • PGTSimMosaic.sim_from_haps()
    • PGTSimSegmental
      • PGTSimSegmental.__init__()
      • PGTSimSegmental.seg_aneuploidy()
      • PGTSimSegmental.sim_haplotype_paths_segmental()
      • PGTSimSegmental.sim_b_allele_freq_segmental()
      • PGTSimSegmental.sim_read_counts_segmental()
      • PGTSimSegmental.full_segmental_sim()
      • PGTSimSegmental.sim_from_haps()
    • PGTSimVCF
      • PGTSimVCF.__init__()
      • PGTSimVCF.gen_parental_haplotypes()
    • PGTSimBase
      • PGTSimBase.__init__()
      • PGTSimBase.draw_parental_genotypes()
      • PGTSimBase.create_genotyping_errors()
      • PGTSimBase.create_switch_errors_help()
      • PGTSimBase.create_switch_errors()
      • PGTSimBase.sim_haplotype_paths()
      • PGTSimBase.sim_haplotype_paths_upd()
      • PGTSimBase.sim_b_allele_freq()
      • PGTSimBase.sim_logR_ratio()
      • PGTSimBase.sim_read_counts()
      • PGTSimBase.sim_joint_het()
      • PGTSimBase.sim_haplotype_ref_panel()
  • I/O Utilities
    • DataReader
      • DataReader.__init__()
      • DataReader.read_data_np()
      • DataReader.read_data_df()
      • DataReader.read_data()

Indices and tables

• Index

• Module Index

• Search Page