Index

A

add_chromosome() (pydigree.genotypes.chromosometemplate.ChromosomeSet method) (pydigree.pedigreecollection.PedigreeCollection method) (pydigree.population.Population method) add_dummy_polygene_chromosomes() (pydigree.simulation.trait.QuantitativeTrait method) add_effect() (pydigree.simulation.trait.QuantitativeTrait method) add_fixed_effects() (pydigree.stats.mixedmodel.mixedmodel.MixedModel method) add_founder_genotype_hook() (pydigree.simulation.genedrop.simulation.GeneDroppingSimulation method) add_founders() (pydigree.population.Population method) add_genetic_effect() (pydigree.stats.mixedmodel.mixedmodel.MixedModel method) add_genotype() (pydigree.genotypes.chromosometemplate.ChromosomeTemplate method) add_genotype_constraint() (pydigree.simulation.genedrop.simulation.GeneDroppingSimulation method) add_ibd_constraint() (pydigree.simulation.genedrop.simulation.GeneDroppingSimulation method) add_pedigree() (pydigree.pedigreecollection.PedigreeCollection method) add_random_effect() (pydigree.stats.mixedmodel.mixedmodel.MixedModel method) add_span() (pydigree.genotypes.labelledalleles.LabelledAlleles method) additive_genetic_variance (pydigree.simulation.trait.QuantitativeTrait attribute) additive_relationship_matrix() (pydigree.pedigree.Pedigree method) (pydigree.pedigreecollection.PedigreeCollection method) advance_generation() (pydigree.population.Population method) ai_element() (pydigree.stats.mixedmodel.likelihood.ML method) (pydigree.stats.mixedmodel.likelihood.REML method) all() (pydigree.cydigree.datastructures.SparseArray method) (pydigree.cydigree.sparsearray.SparseArray method)

all_same_type() (in module pydigree.cydigree.cyfuncs) allele_frequency() (pydigree.individualcontainer.IndividualContainer method) allele_list() (pydigree.individualcontainer.IndividualContainer method) AlleleContainer (class in pydigree.genotypes.genoabc) Alleles (class in pydigree.genotypes.alleles) alleles (pydigree.io.beagle.BeagleMarkerRecord attribute) alleles() (pydigree.individualcontainer.IndividualContainer method) alpha (pydigree.simulation.trait.QuantitativeGeneticEffect attribute) alternates (pydigree.io.beagle.BeagleMarkerRecord attribute) ancestor (pydigree.genotypes.labelledalleles.AncestralAllele attribute) (pydigree.genotypes.labelledalleles.InheritanceSpan attribute) ancestors() (pydigree.individual.Individual method) ancestral_allele (pydigree.genotypes.labelledalleles.InheritanceSpan attribute) ancestral_chromosome (pydigree.genotypes.labelledalleles.InheritanceSpan attribute) AncestralAllele (class in pydigree.genotypes.labelledalleles) any() (pydigree.cydigree.datastructures.SparseArray method) (pydigree.cydigree.sparsearray.SparseArray method) append() (pydigree.sgs.sgs.SGS method) apply() (pydigree.individualcontainer.IndividualContainer method) apply_inplace() (pydigree.individualcontainer.IndividualContainer method) assign_genorow() (in module pydigree.cydigree.vcfparse) average_information_matrix() (pydigree.stats.mixedmodel.likelihood.REML method)

B

BeagleGenotypeRecord (class in pydigree.io.beagle) BeagleMarkerRecord (class in pydigree.io.beagle) bic (pydigree.stats.mixedmodel.mixedmodel.MixedModel attribute)

bit_size() (pydigree.pedigree.Pedigree method) blup() (pydigree.stats.mixedmodel.mixedmodel.MixedModel method) bp_locations (pydigree.io.sgs.GermlineRecord attribute)

C

children_possible() (pydigree.simulation.mating.MatingClique method) choice() (in module pydigree.rand) chromosome (pydigree.sgs.sgs.Segment attribute) chromosome() (pydigree.simulation.chromosomepool.ChromosomePool method) chromosome_count() (pydigree.population.Population method) chromosomeidx (pydigree.genotypes.labelledalleles.InheritanceSpan attribute) ChromosomePool (class in pydigree.simulation.chromosomepool) chromosomes (pydigree.individual.Individual attribute) (pydigree.pedigreecollection.PedigreeCollection attribute) ChromosomeSet (class in pydigree.genotypes.chromosometemplate) ChromosomeTemplate (class in pydigree.genotypes.chromosometemplate) chromwide_ibd() (pydigree.sgs.sgs.SGSAnalysis method) chromwide_ibs() (in module pydigree.ibs) clear() (pydigree.cydigree.datastructures.IntTree method) (pydigree.cydigree.sparsearray.SparseArray method) (pydigree.phenotypes.Phenotypes method) clear_genotypes() (pydigree.individual.Individual method) (pydigree.individualcontainer.IndividualContainer method) clear_model() (pydigree.stats.mixedmodel.mixedmodel.MixedModel method) clear_range() (pydigree.cydigree.sparsearray.SparseArray method) closest_marker() (pydigree.genotypes.chromosometemplate.ChromosomeTemplate method)

cmp_single() (pydigree.cydigree.sparsearray.SparseArray method) common_ancestors() (in module pydigree.paths) connect_individuals() (in module pydigree.io.base) constrained_gamete() (pydigree.individual.Individual method) ConstrainedMendelianSimulation (class in pydigree.simulation.genedrop.constrained_mendelian) container (pydigree.cydigree.datastructures.SparseArray attribute) contains() (pydigree.genotypes.labelledalleles.InheritanceSpan method) (pydigree.sgs.sgs.Segment method) copy() (pydigree.cydigree.datastructures.SparseArray method) (pydigree.cydigree.sparsearray.SparseArray method) (pydigree.genotypes.sparsealleles.SparseAlleles method) (pydigree.stats.mixedmodel.mixedmodel.MixedModel method) copy_span() (pydigree.genotypes.alleles.Alleles method) (pydigree.genotypes.genoabc.AlleleContainer method) (pydigree.genotypes.labelledalleles.LabelledAlleles method) (pydigree.genotypes.sparsealleles.SparseAlleles method) count() (in module pydigree.common) covariance_matrices (pydigree.stats.mixedmodel.mixedmodel.MixedModel attribute) covariance_matrix (pydigree.stats.mixedmodel.mixedmodel.RandomEffect attribute) create_individual() (pydigree.io.base.PEDRecord method) create_pop_handler_func() (in module pydigree.io.plink) cumsum() (in module pydigree.common)

D

data (pydigree.cydigree.sparsearray.SparseArray attribute) (pydigree.io.beagle.BeagleGenotypeRecord attribute) delabel() (pydigree.genotypes.labelledalleles.LabelledAlleles method) delabel_genotypes() (pydigree.individual.Individual method) delete() (pydigree.cydigree.datastructures.IntTree method) delete_phenotype() (pydigree.individual.Individual method) (pydigree.individualcontainer.IndividualContainer method) (pydigree.phenotypes.Phenotypes method) delrange() (pydigree.cydigree.datastructures.IntTree method) dense_cmp() (pydigree.cydigree.sparsearray.SparseArray method)

density() (pydigree.cydigree.sparsearray.SparseArray method) depth (pydigree.individual.Individual attribute) descendants() (pydigree.individual.Individual method) df (pydigree.stats.mixedmodel.mixedmodel.MixedModel attribute) direct_to_disk() (pydigree.sgs.sgs.SGSAnalysis static method) dominance_relationship_matrix() (pydigree.pedigree.Pedigree method) (pydigree.pedigreecollection.PedigreeCollection method) dtype (pydigree.genotypes.labelledalleles.LabelledAlleles attribute) (pydigree.genotypes.sparsealleles.SparseAlleles attribute) dtype() (pydigree.genotypes.genoabc.AlleleContainer method)

E

empty() (pydigree.cydigree.datastructures.IntTree method) (pydigree.genotypes.sparsealleles.SparseAlleles static method) empty_chromosome() (pydigree.genotypes.chromosometemplate.ChromosomeTemplate method) empty_like() (pydigree.genotypes.alleles.Alleles method) (pydigree.genotypes.genoabc.AlleleContainer method) (pydigree.genotypes.labelledalleles.LabelledAlleles method) (pydigree.genotypes.sparsealleles.SparseAlleles method) environmental_variance (pydigree.simulation.trait.QuantitativeTrait attribute)

eq_single() (pydigree.cydigree.sparsearray.SparseArray method) evolve() (pydigree.simulation.chromosomepool.ChromosomePool method) expectation_maximization() (in module pydigree.stats.mixedmodel.maximization) (pydigree.stats.mixedmodel.likelihood.ML method) (pydigree.stats.mixedmodel.likelihood.REML method) expected_genotypic_value (pydigree.simulation.trait.QuantitativeGeneticEffect attribute) (pydigree.simulation.trait.QuantitativeTrait attribute) exponential_growth() (in module pydigree.population) extend() (pydigree.sgs.sgs.SGS method)

F

fastfirstitem() (in module pydigree.cydigree.cyfuncs) females() (pydigree.individualcontainer.IndividualContainer method) fertilize() (pydigree.individual.Individual static method) FileFormatError filter_segments() (in module pydigree.sgs.sgs) finalize() (pydigree.genotypes.chromosometemplate.ChromosomeSet method) (pydigree.genotypes.chromosometemplate.ChromosomeTemplate method) find() (pydigree.cydigree.datastructures.IntTree method) fisher_element() (pydigree.stats.mixedmodel.likelihood.ML method) (pydigree.stats.mixedmodel.likelihood.REML method) fisher_information_matrix() (pydigree.stats.mixedmodel.likelihood.REML method) fit() (pydigree.stats.variancecomponents.VarianceComponentsLinkage method) fit_alternative_model() (pydigree.stats.variancecomponents.VarianceComponentsLinkage method) fit_model() (pydigree.stats.mixedmodel.mixedmodel.MixedModel method) fit_null_model() (pydigree.stats.variancecomponents.VarianceComponentsLinkage method) fix() (pydigree.simulation.chromosomepool.ChromosomePool method) flatten() (in module pydigree.common) form_cliques() (pydigree.simulation.mating.MonogamousMating method)

founder_chromosome() (pydigree.genotypes.labelledalleles.LabelledAlleles static method) founder_individual() (pydigree.population.Population method) founders() (pydigree.individualcontainer.IndividualContainer method) fraternity() (in module pydigree.paths) (pydigree.pedigree.Pedigree method) frequency() (pydigree.genotypes.chromosometemplate.ChromosomeSet method) from_dense() (pydigree.cydigree.datastructures.SparseArray static method) (pydigree.cydigree.sparsearray.SparseArray static method) from_file() (pydigree.simulation.trait.QuantitativeTrait static method) from_genomesimla() (pydigree.genotypes.chromosometemplate.ChromosomeTemplate static method) from_items() (pydigree.cydigree.datastructures.SparseArray static method) (pydigree.cydigree.sparsearray.SparseArray static method) from_keys() (pydigree.cydigree.datastructures.IntTree static method) from_numpy() (pydigree.cydigree.datastructures.SparseArray static method) from_pairs() (pydigree.cydigree.datastructures.IntTree static method) from_population() (pydigree.simulation.chromosomepool.ChromosomePool static method) full_label (pydigree.individual.Individual attribute) full_loglikelihood() (in module pydigree.stats.mixedmodel.likelihood)

G

G (pydigree.stats.mixedmodel.mixedmodel.RandomEffect attribute) gamete() (pydigree.individual.Individual method) GeneDroppingSimulation (class in pydigree.simulation.genedrop.simulation) genotype_as_phenotype() (pydigree.individual.Individual method) (pydigree.individualcontainer.IndividualContainer method) genotype_missingness() (pydigree.individualcontainer.IndividualContainer method) genotypes() (pydigree.io.vcf.VCFRecord method) genotypes_from_sequential_alleles() (in module pydigree.io.base) genotypic_value() (pydigree.simulation.trait.QuantitativeGeneticEffect method) GermlineRecord (class in pydigree.io.sgs) get() (pydigree.cydigree.datastructures.IntTree method) (pydigree.phenotypes.Phenotypes method) get_constrained_genotypes() (pydigree.individual.Individual method) get_female() (pydigree.simulation.mating.MatingClique method) get_founder_genotypes() (pydigree.individualcontainer.IndividualContainer method) (pydigree.population.Population method) (pydigree.simulation.genedrop.simulation.GeneDroppingSimulation method)

get_genotype() (pydigree.individual.Individual method) get_genotype_set() (pydigree.simulation.chromosomepool.ChromosomePool method) get_genotypes() (pydigree.individual.Individual method) (pydigree.individualcontainer.IndividualContainer method) (pydigree.population.Population method) get_ibs_states() (in module pydigree.ibs) get_item() (pydigree.cydigree.sparsearray.SparseArray method) get_linkage_equilibrium_genotypes() (pydigree.population.Population method) get_male() (pydigree.simulation.mating.MatingClique method) get_slice() (pydigree.cydigree.sparsearray.SparseArray method) getitems() (pydigree.io.vcf.VCFRecord method) getrange() (pydigree.cydigree.datastructures.IntTree method) gradient() (pydigree.stats.mixedmodel.likelihood.MixedModelLikelihood method) (pydigree.stats.mixedmodel.likelihood.REML method) gradient_element() (pydigree.stats.mixedmodel.likelihood.ML method) grid() (in module pydigree.stats.mathfuncs) grid_search() (in module pydigree.stats.mixedmodel.maximization) grouper() (in module pydigree.common)

H

haplotype (pydigree.genotypes.labelledalleles.AncestralAllele attribute) (pydigree.genotypes.labelledalleles.InheritanceSpan attribute) has_allele() (pydigree.individual.Individual method)

has_genotypes() (pydigree.individual.Individual method) has_phenotype() (pydigree.phenotypes.Phenotypes method) hessian_element() (pydigree.stats.mixedmodel.likelihood.ML method) (pydigree.stats.mixedmodel.likelihood.REML method)

I

ibd_matrix() (pydigree.sgs.sgs.SGSAnalysis method) ibd_state() (pydigree.sgs.sgs.SGS method) (pydigree.sgs.sgs.SGSAnalysis method) ibs() (in module pydigree.cydigree.cyfuncs) identifier (pydigree.io.beagle.BeagleGenotypeRecord attribute) inbreeding() (pydigree.individual.Individual method) (pydigree.pedigree.Pedigree method) incidence_matrix (pydigree.stats.mixedmodel.mixedmodel.RandomEffect attribute) incidence_matrix() (pydigree.stats.mixedmodel.mixin.MixedModelMixin method) ind1 (pydigree.sgs.sgs.Segment attribute) ind2 (pydigree.sgs.sgs.Segment attribute) indices (pydigree.cydigree.datastructures.SparseArray attribute) Individual (class in pydigree.individual) IndividualContainer (class in pydigree.individualcontainer) individuals (pydigree.pedigreecollection.PedigreeCollection attribute) (pydigree.population.Population attribute) (pydigree.sgs.sgs.SGSAnalysis attribute) info (pydigree.io.vcf.VCFRecord attribute) info_matrix() (pydigree.stats.mixedmodel.likelihood.MixedModelLikelihood method) (pydigree.stats.mixedmodel.likelihood.REML method) InheritanceSpan (class in pydigree.genotypes.labelledalleles) initialize_pool() (pydigree.simulation.chromosomepool.ChromosomePool method) insert() (pydigree.cydigree.datastructures.IntTree method)

intercept (pydigree.simulation.trait.QuantitativeTrait attribute) interleave() (in module pydigree.cydigree.cyfuncs) intersection() (pydigree.cydigree.datastructures.IntTree method) interval (pydigree.genotypes.labelledalleles.InheritanceSpan attribute) intervals_to_array() (in module pydigree.sgs.sgs) IntTree (class in pydigree.cydigree.datastructures) inv() (in module pydigree.stats.mixedmodel.likelihood) (in module pydigree.stats.mixedmodel.mixedmodel) invert_dict() (in module pydigree.common) is_founder() (pydigree.individual.Individual method) is_genetic_effect() (in module pydigree.stats.mixedmodel.mixedmodel) is_marryin_founder() (pydigree.individual.Individual method) is_missing_genotype() (in module pydigree.individual) (in module pydigree.population) is_phenotype_record() (pydigree.io.beagle.BeagleGenotypeRecord method) is_positive_definite() (in module pydigree.stats.mathfuncs) is_sorted() (in module pydigree.cydigree.cyfuncs) items() (pydigree.cydigree.datastructures.SparseArray method) (pydigree.cydigree.sparsearray.SparseArray method) (pydigree.phenotypes.Phenotypes method) iterate_pool() (pydigree.simulation.chromosomepool.ChromosomePool method) IterationError iterinfo() (pydigree.genotypes.chromosometemplate.ChromosomeTemplate method)

J

join_gaps() (in module pydigree.sgs.sgs)

K

keys() (pydigree.cydigree.datastructures.IntTree method) (pydigree.cydigree.datastructures.SparseArray method) (pydigree.cydigree.sparsearray.SparseArray method) (pydigree.genotypes.sparsealleles.SparseAlleles method) (pydigree.pedigreecollection.PedigreeCollection method) (pydigree.phenotypes.Phenotypes method)

kinship() (in module pydigree.paths) (pydigree.pedigree.Pedigree method)

L

label (pydigree.io.beagle.BeagleGenotypeRecord attribute) (pydigree.io.beagle.BeagleMarkerRecord attribute) (pydigree.stats.mixedmodel.mixedmodel.RandomEffect attribute) label_genotypes() (pydigree.individual.Individual method) LabelledAlleles (class in pydigree.genotypes.labelledalleles) levels (pydigree.stats.mixedmodel.mixedmodel.RandomEffect attribute) LikelihoodRatioTest() (in module pydigree.stats.stattests) LikelihoodRatioTestResult (class in pydigree.stats.stattests) linkageequilibrium_chromosome() (pydigree.genotypes.chromosometemplate.ChromosomeTemplate method) linkageequilibrium_chromosomes() (pydigree.genotypes.chromosometemplate.ChromosomeTemplate method) location (pydigree.io.sgs.GermlineRecord attribute)

locus_additive_variance (pydigree.simulation.trait.QuantitativeGeneticEffect attribute) locus_dominance_variance (pydigree.simulation.trait.QuantitativeGeneticEffect attribute) lod (pydigree.stats.stattests.LikelihoodRatioTestResult attribute) log_base_change() (in module pydigree.common) logdet() (in module pydigree.stats.mixedmodel.likelihood) logical_not() (pydigree.cydigree.datastructures.SparseArray method) (pydigree.cydigree.sparsearray.SparseArray method) logistic_growth() (in module pydigree.population) loglikelihood() (pydigree.stats.mixedmodel.likelihood.ML method) (pydigree.stats.mixedmodel.likelihood.REML method) (pydigree.stats.mixedmodel.mixedmodel.MixedModel method)

M

major_allele() (pydigree.individualcontainer.IndividualContainer method) make_incidence_matrix() (in module pydigree.stats.mixedmodel.mixedmodel) make_intervals() (in module pydigree.sgs.sgs) makeP() (in module pydigree.stats.mixedmodel.likelihood) makeVinv() (in module pydigree.stats.mixedmodel.likelihood) males() (pydigree.individualcontainer.IndividualContainer method) marker_label() (pydigree.genotypes.chromosometemplate.ChromosomeSet method) marker_labels (pydigree.cydigree.cyfuncs.Segment attribute) (pydigree.sgs.sgs.Segment attribute) mate() (pydigree.population.Population method) (pydigree.simulation.mating.MatingClique method) MatingClique (class in pydigree.simulation.mating) MatingStructure (class in pydigree.simulation.mating) matriline() (pydigree.individual.Individual method) maximize() (pydigree.stats.mixedmodel.mixedmodel.MixedModel method) maximized (pydigree.stats.mixedmodel.mixedmodel.MixedModel attribute)

merge() (pydigree.sgs.sgs.SGSAnalysis method) merge_dicts() (in module pydigree.common) missing (pydigree.genotypes.alleles.Alleles attribute) (pydigree.genotypes.sparsealleles.SparseAlleles attribute) (pydigree.sgs.sgs.Segment attribute) missing_rate (pydigree.sgs.sgs.Segment attribute) missingcode (pydigree.genotypes.alleles.Alleles attribute) (pydigree.genotypes.sparsealleles.SparseAlleles attribute) mitochondrial_relationship_matrix() (pydigree.pedigree.Pedigree method) (pydigree.pedigreecollection.PedigreeCollection method) MixedModel (class in pydigree.stats.mixedmodel.mixedmodel) MixedModelLikelihood (class in pydigree.stats.mixedmodel.likelihood) MixedModelMixin (class in pydigree.stats.mixedmodel.mixin) ML (class in pydigree.stats.mixedmodel.likelihood) MLEResult (class in pydigree.stats.mixedmodel.maximization) mode() (in module pydigree.common) MonogamousMating (class in pydigree.simulation.mating)

N

NaiveGeneDroppingSimulation (class in pydigree.simulation.genedrop.naivegenedrop) nchrom() (pydigree.genotypes.chromosometemplate.ChromosomeSet method) ndense() (pydigree.cydigree.sparsearray.SparseArray method) newtonlike_maximization() (in module pydigree.stats.mixedmodel.maximization) next_generation() (pydigree.simulation.mating.MatingStructure method) (pydigree.simulation.mating.RandomMating method) nlevels (pydigree.stats.mixedmodel.mixedmodel.RandomEffect attribute) nloci() (pydigree.genotypes.chromosometemplate.ChromosomeSet method)

nmark (pydigree.cydigree.cyfuncs.Segment attribute) (pydigree.sgs.sgs.Segment attribute) nmark() (pydigree.genotypes.alleles.Alleles method) (pydigree.genotypes.chromosometemplate.ChromosomeTemplate method) (pydigree.genotypes.sparsealleles.SparseAlleles method) nobs() (pydigree.stats.mixedmodel.mixedmodel.MixedModel method) NodeStack (class in pydigree.cydigree.datastructures) nonfounders() (pydigree.individualcontainer.IndividualContainer method) NotMeaningfulError

O

observations() (pydigree.stats.mixedmodel.mixedmodel.MixedModel method) observed_element() (pydigree.stats.mixedmodel.likelihood.ML method) (pydigree.stats.mixedmodel.likelihood.REML method)

outputlabel (pydigree.genotypes.chromosometemplate.ChromosomeTemplate attribute)

P

P (pydigree.stats.mixedmodel.mixedmodel.MixedModel attribute) pair (pydigree.io.sgs.GermlineRecord attribute) parents() (pydigree.individual.Individual method) path_downward() (in module pydigree.paths) paths() (in module pydigree.paths) paths_through_ancestor() (in module pydigree.paths) patriline() (pydigree.individual.Individual method) Pedigree (class in pydigree.pedigree) PedigreeCollection (class in pydigree.pedigreecollection) pedigrees (pydigree.pedigreecollection.PedigreeCollection attribute) PEDRecord (class in pydigree.io.base) phenotype_dataframe() (pydigree.individualcontainer.IndividualContainer method) Phenotypes (class in pydigree.phenotypes) phenotypes() (pydigree.individualcontainer.IndividualContainer method) physical_location (pydigree.sgs.sgs.Segment attribute) physical_map() (pydigree.genotypes.chromosometemplate.ChromosomeSet method) physical_position (pydigree.cydigree.cyfuncs.Segment attribute) physical_size (pydigree.sgs.sgs.Segment attribute) physical_start (pydigree.cydigree.cyfuncs.Segment attribute) physical_stop (pydigree.cydigree.cyfuncs.Segment attribute) plink_data_handler() (in module pydigree.io.plink) Population (class in pydigree.population) pos (pydigree.io.beagle.BeagleMarkerRecord attribute) predict_phenotype() (pydigree.individual.Individual method) (pydigree.individualcontainer.IndividualContainer method) (pydigree.simulation.trait.QuantitativeTrait method) predicted_trait_accuracy() (pydigree.simulation.genedrop.simulation.GeneDroppingSimulation method) print_sizes() (in module pydigree.cydigree.datastructures) product() (in module pydigree.common) pvalue (pydigree.stats.stattests.LikelihoodRatioTestResult attribute) pydigree (module) pydigree.common (module) pydigree.cydigree (module) pydigree.cydigree.cyfuncs (module) pydigree.cydigree.datastructures (module) pydigree.cydigree.sparsearray (module) pydigree.cydigree.vcfparse (module) pydigree.datastructures (module) pydigree.exceptions (module) pydigree.genotypes (module) pydigree.genotypes.alleles (module)

pydigree.genotypes.chromosometemplate (module) pydigree.genotypes.genoabc (module) pydigree.genotypes.labelledalleles (module) pydigree.genotypes.sparsealleles (module) pydigree.ibs (module) pydigree.individual (module) pydigree.individualcontainer (module) pydigree.io (module) pydigree.io.base (module) pydigree.io.beagle (module) pydigree.io.genomesimla (module) pydigree.io.kinship (module) pydigree.io.plink (module) pydigree.io.sgs (module) pydigree.io.smartopen (module) pydigree.io.vcf (module) pydigree.paths (module) pydigree.pedigree (module) pydigree.pedigreecollection (module) pydigree.phenotypes (module) pydigree.population (module) pydigree.rand (module) pydigree.recombination (module) pydigree.sgs (module) pydigree.sgs.sgs (module) pydigree.simulation (module) pydigree.simulation.chromosomepool (module) pydigree.simulation.genedrop (module) pydigree.simulation.genedrop.constrained_mendelian (module) pydigree.simulation.genedrop.naivegenedrop (module) pydigree.simulation.genedrop.simulation (module) pydigree.simulation.mating (module) pydigree.simulation.trait (module) pydigree.stats (module) pydigree.stats.mathfuncs (module) pydigree.stats.mixedmodel (module) pydigree.stats.mixedmodel.likelihood (module) pydigree.stats.mixedmodel.maximization (module) pydigree.stats.mixedmodel.mixedmodel (module) pydigree.stats.mixedmodel.mixin (module) pydigree.stats.stattests (module) pydigree.stats.variancecomponents (module)

Q

QuantitativeGeneticEffect (class in pydigree.simulation.trait)

QuantitativeTrait (class in pydigree.simulation.trait)

R

R (pydigree.stats.mixedmodel.mixedmodel.MixedModel attribute) random_choice() (in module pydigree.common) RandomEffect (class in pydigree.stats.mixedmodel.mixedmodel) RandomMating (class in pydigree.simulation.mating) read_beagle() (in module pydigree.io.beagle) read_beagle_genotypefile() (in module pydigree.io.beagle) read_beagle_markerfile() (in module pydigree.io.beagle) read_constraints() (pydigree.simulation.genedrop.simulation.GeneDroppingSimulation method) read_germline() (in module pydigree.io.sgs) read_gs_chromosome_template() (in module pydigree.io.genomesimla) read_kinship() (in module pydigree.io.kinship) read_map() (in module pydigree.io.plink) read_ped() (in module pydigree.io.base) read_phenotypes() (in module pydigree.io.base) read_plink() (in module pydigree.io.plink) read_vcf() (in module pydigree.io.vcf) recombine() (in module pydigree.recombination) ref (pydigree.cydigree.sparsearray.SparseArray attribute) refcode (pydigree.cydigree.datastructures.SparseArray attribute) (pydigree.genotypes.sparsealleles.SparseAlleles attribute)

reference (pydigree.io.beagle.BeagleMarkerRecord attribute) register_child() (pydigree.individual.Individual method) register_individual() (pydigree.population.Population method) register_with_parents() (pydigree.individual.Individual method) REML (class in pydigree.stats.mixedmodel.likelihood) remove_ancestry() (pydigree.individual.Individual method) (pydigree.population.Population method) remove_individual() (pydigree.population.Population method) replicate() (pydigree.simulation.genedrop.constrained_mendelian.ConstrainedMendelianSimulation method) (pydigree.simulation.genedrop.naivegenedrop.NaiveGeneDroppingSimulation method) (pydigree.simulation.genedrop.simulation.GeneDroppingSimulation method) rescale() (pydigree.simulation.trait.QuantitativeTrait method) residual_variance() (pydigree.stats.mixedmodel.mixedmodel.MixedModel method) richards() (in module pydigree.simulation.chromosomepool) run() (pydigree.simulation.genedrop.simulation.GeneDroppingSimulation method) run_founder_genotype_hooks() (pydigree.simulation.genedrop.simulation.GeneDroppingSimulation method) runs() (in module pydigree.cydigree.cyfuncs) runs_gte() (in module pydigree.cydigree.cyfuncs) runs_gte_uint8() (in module pydigree.cydigree.cyfuncs)

S

sample_with_replacement() (in module pydigree.rand) scoring_iteration() (in module pydigree.stats.mixedmodel.maximization) Segment (class in pydigree.cydigree.cyfuncs) (class in pydigree.sgs.sgs) segments (pydigree.sgs.sgs.SGSAnalysis attribute) select_random_loci() (pydigree.genotypes.chromosometemplate.ChromosomeSet method) set_frequency() (pydigree.genotypes.chromosometemplate.ChromosomeTemplate method) set_genotype() (pydigree.individual.Individual method) set_info() (pydigree.stats.mixedmodel.likelihood.MixedModelLikelihood method) set_intervals_to_value() (in module pydigree.cydigree.cyfuncs) set_item() (pydigree.cydigree.datastructures.SparseArray method) (pydigree.cydigree.sparsearray.SparseArray method) set_liability_threshold() (pydigree.simulation.trait.QuantitativeTrait method) set_outcome() (pydigree.stats.mixedmodel.mixedmodel.MixedModel method) set_parameters() (pydigree.stats.mixedmodel.likelihood.MixedModelLikelihood method) set_seed() (in module pydigree.rand) set_trait() (pydigree.simulation.genedrop.simulation.GeneDroppingSimulation method) set_variance_components() (pydigree.stats.mixedmodel.mixedmodel.MixedModel method) sex_ratio() (pydigree.individualcontainer.IndividualContainer method) SGS (class in pydigree.sgs.sgs) sgs_autozygous() (in module pydigree.sgs.sgs) sgs_population() (in module pydigree.sgs.sgs) sgs_unphased() (in module pydigree.sgs.sgs) SGSAnalysis (class in pydigree.sgs.sgs) siblings() (pydigree.individual.Individual method)

sigma (pydigree.stats.mixedmodel.mixedmodel.RandomEffect attribute) simulate_ibd_states() (pydigree.pedigree.Pedigree method) SimulationError size (pydigree.cydigree.datastructures.SparseArray attribute) (pydigree.cydigree.sparsearray.SparseArray attribute) size() (pydigree.cydigree.datastructures.IntTree method) (pydigree.genotypes.chromosometemplate.ChromosomeTemplate method) (pydigree.population.Population method) (pydigree.simulation.chromosomepool.ChromosomePool method) smartopen() (in module pydigree.io.smartopen) sort_pedigrees() (in module pydigree.io.base) sparse_cmp() (pydigree.cydigree.sparsearray.SparseArray method) sparse_eq() (pydigree.cydigree.sparsearray.SparseArray method) SparseAlleles (class in pydigree.genotypes.sparsealleles) SparseArray (class in pydigree.cydigree.datastructures) (class in pydigree.cydigree.sparsearray) sparsity() (pydigree.cydigree.datastructures.SparseArray method) (pydigree.cydigree.sparsearray.SparseArray method) start (pydigree.cydigree.cyfuncs.Segment attribute) (pydigree.genotypes.labelledalleles.InheritanceSpan attribute) (pydigree.sgs.sgs.Segment attribute) stop (pydigree.cydigree.cyfuncs.Segment attribute) (pydigree.genotypes.labelledalleles.InheritanceSpan attribute) (pydigree.sgs.sgs.Segment attribute) summary() (pydigree.stats.mixedmodel.mixedmodel.MixedModel method)

T

table() (in module pydigree.common) to_germline() (pydigree.sgs.sgs.Segment method) to_series() (pydigree.phenotypes.Phenotypes method) to_stack() (pydigree.cydigree.datastructures.IntTree method) to_tuple() (pydigree.genotypes.labelledalleles.InheritanceSpan method)

todense() (pydigree.genotypes.sparsealleles.SparseAlleles method) tolist() (pydigree.cydigree.datastructures.SparseArray method) (pydigree.cydigree.sparsearray.SparseArray method) (pydigree.cydigree.vcfparse.VariantStack method) total_variance (pydigree.simulation.trait.QuantitativeTrait attribute) traverse() (pydigree.cydigree.datastructures.IntTree method)

U

union() (pydigree.cydigree.datastructures.IntTree method) update() (pydigree.individual.Individual method) (pydigree.pedigreecollection.PedigreeCollection method) (pydigree.phenotypes.Phenotypes method) (pydigree.population.Population method)

update_segment_references() (pydigree.sgs.sgs.SGSAnalysis method)

V

V_i (pydigree.stats.mixedmodel.mixedmodel.RandomEffect attribute) values() (pydigree.cydigree.datastructures.IntTree method) (pydigree.cydigree.datastructures.SparseArray method) (pydigree.cydigree.sparsearray.SparseArray method) (pydigree.genotypes.sparsealleles.SparseAlleles method) (pydigree.phenotypes.Phenotypes method) variance_component (pydigree.stats.mixedmodel.mixedmodel.RandomEffect attribute)

variance_components (pydigree.stats.mixedmodel.mixedmodel.MixedModel attribute) VarianceComponentsLinkage (class in pydigree.stats.variancecomponents) VarianceComponentsLinkageResult (class in pydigree.stats.variancecomponents) VariantStack (class in pydigree.cydigree.vcfparse) vcf_allele_parser() (in module pydigree.cydigree.vcfparse) VCFRecord (class in pydigree.io.vcf) verify() (pydigree.cydigree.datastructures.IntTree method)

W

write_data() (pydigree.simulation.genedrop.simulation.GeneDroppingSimulation method) write_map() (in module pydigree.io.plink) write_ped() (in module pydigree.io.plink)

write_pedigree() (in module pydigree.io.base) write_phenotypes() (in module pydigree.io.base) write_plink() (in module pydigree.io.plink) write_sgs() (in module pydigree.io.sgs)

Z

Z (pydigree.stats.mixedmodel.mixedmodel.RandomEffect attribute)