Index

_

_fid (xftsim.ped.Pedigree attribute)

_generation (xftsim.ped.Pedigree attribute) _generational_depth (xftsim.ped.Pedigree attribute)

A

accepts_grouping (xftsim.arch.AggregationComponent attribute), [1] (xftsim.arch.ArchComponent attribute), [1], [2], [3] (xftsim.arch.CNoiseComponent attribute), [1] (xftsim.arch.GeneticComponent attribute), [1] (xftsim.arch.HaplotypeGeneticComponent attribute), [1] (xftsim.arch.NoiseComponent attribute), [1] (xftsim.arch.ThresholdComponent attribute) add() (xftsim.arch.Architecture method), [1] AdditiveEffects (class in xftsim.effect), [1] af (xftsim.gwas.GWASResult attribute), [1] (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) (xftsim.index.HaploidVariantIndex attribute) (xftsim.struct.DenseHaplotypeArray property) (xftsim.struct.VariantMeta attribute) af_empirical (xftsim.struct.DenseHaplotypeArray property) (xftsim.struct.HaplotypeArrayAccessor property) AggregationComponent (class in xftsim.arch), [1] annotate() (xftsim.index.DiploidVariantIndex method)

annotation (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) annotation_array (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) annotation_names (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) apply() (xftsim.filters.AscertainmentFilter method) (xftsim.filters.Filter method) (xftsim.filters.SibPairFilter method) (xftsim.filters.SubsampleFilter method) (xftsim.filters.TrioFilter method) (xftsim.filters.UnrelatedFilter method) ArchComponent (class in xftsim.arch), [1] Architecture (class in xftsim.arch), [1] ArchNode (class in xftsim.arch), [1] AscertainedView (class in xftsim.filters) ascertainment_key (xftsim.filters.AscertainedView attribute), [1] AscertainmentFilter (class in xftsim.filters) at_most() (xftsim.index.XftIndex method) attrs (xftsim.struct.DenseHaplotypeArray property)

B

BatchedMating (class in xftsim.mate), [1] beta (xftsim.gwas.GWASResult attribute), [1]

build_simulation_from_config() (in module xftsim.cli) BUILTINS (in module xftsim.arch), [1]

C

cartesian_product() (in module xftsim.utils) chrom (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) (xftsim.index.HaploidVariantIndex attribute) (xftsim.struct.DenseHaplotypeArray property) (xftsim.struct.VariantMeta attribute) chroms (xftsim.struct.GeneticMap attribute) CNoiseComponent (class in xftsim.arch), [1] comp_type (xftsim.index.ComponentIndex property) component (xftsim.arch.ArchNode attribute), [1] component_name (xftsim.index.ComponentIndex attribute) (xftsim.index.ComponentIndex property) ComponentIndex (class in xftsim.index) compute() (xftsim.arch.AggregationComponent method), [1] (xftsim.arch.ArchComponent method), [1] (xftsim.arch.Architecture method), [1] (xftsim.arch.CNoiseComponent method), [1] (xftsim.arch.GeneticComponent method), [1] (xftsim.arch.HaplotypeGeneticComponent method), [1] (xftsim.arch.NoiseComponent method), [1] (xftsim.arch.ThresholdComponent method)

constant_map() (xftsim.reproduce.RecombinationMap static method) ConstantCount (class in xftsim.utils) continue_run() (xftsim.sim.Simulation method), [1] coord_dict (xftsim.index.XftIndex property) coord_frame (xftsim.index.XftIndex property) coord_index (xftsim.index.XftIndex property) coord_mindex (xftsim.index.XftIndex property) coords (xftsim.index.XftIndex property) cov2cor() (in module xftsim.utils)

D

data (xftsim.struct.DenseHaplotypeArray property) demo() (in module xftsim.cli) DenseHaplotypeArray (class in xftsim.struct) depth (xftsim.index.ComponentIndex attribute) (xftsim.index.ComponentIndex property) diploid_genotypes (xftsim.struct.DenseHaplotypeArray property) diploid_matvec() (xftsim.struct.DenseHaplotypeArray method)

DiploidVariantIndex (class in xftsim.index) draw (xftsim.utils.ConstantCount attribute) (xftsim.utils.MixtureCount attribute) (xftsim.utils.NegativeBinomialCount attribute) (xftsim.utils.VariableCount attribute) (xftsim.utils.ZeroTruncatedPoissonCount attribute) drop_isel() (xftsim.struct.DenseHaplotypeArray method)

E

effects (xftsim.effect.EffectSpec attribute), [1] EffectSpec (class in xftsim.effect), [1] ensure2D() (in module xftsim.utils) estimate() (xftsim.stats.HasemanElstonEstimator method), [1] (xftsim.stats.MatingStatistics method), [1] (xftsim.stats.ParentOffspringRegression method), [1] (xftsim.stats.SampleStatistics method), [1] (xftsim.stats.Statistic method), [1] exhaustive_enumerate() (in module xftsim.utils)

exhaustive_permutation() (in module xftsim.utils) expectation (xftsim.utils.ConstantCount attribute) (xftsim.utils.MixtureCount attribute) (xftsim.utils.NegativeBinomialCount attribute) (xftsim.utils.PoissonCount attribute) (xftsim.utils.VariableCount attribute) (xftsim.utils.VariableCount property) (xftsim.utils.ZeroTruncatedPoissonCount attribute) extra (xftsim.struct.SampleMeta attribute) (xftsim.struct.VariantMeta attribute)

F

father_phenotypes (xftsim.filters.TrioView attribute) FatherComponent (class in xftsim.arch), [1] fid (xftsim.index.SampleIndex attribute) (xftsim.index.SampleIndex property) (xftsim.struct.DenseHaplotypeArray property) (xftsim.struct.SampleMeta attribute) Filter (class in xftsim.filters) filter() (xftsim.index.SampleFilter method) FilteredView (class in xftsim.filters) founder_component (xftsim.arch.FatherComponent attribute) (xftsim.arch.MotherComponent attribute) (xftsim.arch.ParentComponent attribute) founder_haplotypes_from_AFs() (in module xftsim.founders) founder_haplotypes_from_msprime_grg() (in module xftsim.founders) founder_haplotypes_from_plink_bfile() (in module xftsim.founders) founder_haplotypes_from_sgkit_dataset() (in module xftsim.founders) founder_haplotypes_from_stdpopsim_grg() (in module xftsim.founders) founder_haplotypes_uniform_AFs() (in module xftsim.founders)

frame (xftsim.index.XftIndex property) (xftsim.struct.GeneticMap attribute) frame_copy() (xftsim.index.XftIndex method) from_array() (xftsim.effect.AdditiveEffects class method), [1] (xftsim.effect.MultivariateEffects class method), [1] from_arrays() (xftsim.index.ComponentIndex method) (xftsim.index.ComponentIndex static method) from_checkpoint() (xftsim.sim.Simulation class method), [1] from_covg() (xftsim.effect.MultivariateEffects class method), [1] from_formula() (xftsim.arch.Architecture class method), [1] from_frame() (xftsim.index.ComponentIndex method) (xftsim.index.ComponentIndex static method) from_h2() (xftsim.effect.AdditiveEffects class method), [1] (xftsim.effect.SparseEffects class method), [1] from_h2_rg() (xftsim.effect.MultivariateEffects class method), [1] from_haplotypes() (xftsim.reproduce.RecombinationMap static method) from_product() (xftsim.index.ComponentIndex method) (xftsim.index.ComponentIndex static method) from_pyrho_maps() (xftsim.struct.GeneticMap class method)

G

G (xftsim.ped.Pedigree attribute) GeneralAssortativeMating (class in xftsim.mate), [1] generation (xftsim.sim.Simulation attribute), [1] (xftsim.stats.GenerationResult attribute), [1] (xftsim.struct.DenseHaplotypeArray property) (xftsim.struct.GraphHaplotypeOperator property) (xftsim.struct.HaplotypeArrayAccessor property) (xftsim.struct.SampleMeta attribute) generation() (xftsim.ped.Pedigree method) generational_depth (xftsim.ped.Pedigree property) GenerationResult (class in xftsim.stats), [1] generations() (xftsim.ped.Pedigree method)

GeneticComponent (class in xftsim.arch), [1] GeneticMap (class in xftsim.struct) genotypes_to_pseudo_haplotypes() (in module xftsim.io) get_current_generation() (xftsim.ped.Pedigree method) get_most_recent_K_generations() (xftsim.ped.Pedigree method) get_sample_indexer() (xftsim.struct.DenseHaplotypeArray method) (xftsim.struct.HaplotypeArrayAccessor method) get_variant_indexer() (xftsim.struct.DenseHaplotypeArray method) (xftsim.struct.HaplotypeArrayAccessor method) GraphHaplotypeOperator (class in xftsim.struct) grouping (xftsim.arch.ArchNode attribute), [1] GWAS (class in xftsim.gwas) GWASResult (class in xftsim.gwas)

H

HaploidVariantIndex (class in xftsim.index) haplotype_history (xftsim.sim.Simulation attribute), [1] HaplotypeArrayAccessor (class in xftsim.struct) HaplotypeGeneticComponent (class in xftsim.arch), [1] HaplotypeOperator (class in xftsim.struct) haplotypes (xftsim.sim.Simulation property), [1]

haplotypes_from_sgkit_dataset() (in module xftsim.io) HasemanElstonEstimator (class in xftsim.stats), [1] hcopy (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) (xftsim.index.HaploidVariantIndex attribute) hierarchical_subsample() (in module xftsim.utils)

I

ids_from_generation() (in module xftsim.utils) ids_from_generation_range() (in module xftsim.utils) ids_from_n_generation() (in module xftsim.utils) iid (xftsim.index.SampleIndex attribute) (xftsim.index.SampleIndex property) (xftsim.struct.DenseHaplotypeArray property) (xftsim.struct.SampleMeta attribute)

iloc() (xftsim.index.SampleIndex method) (xftsim.index.XftIndex method) indices (xftsim.filters.AscertainedView attribute), [1] (xftsim.filters.SubsampleView attribute), [1] (xftsim.filters.UnrelatedView attribute), [1] info() (in module xftsim.cli) inputs (xftsim.arch.ArchNode attribute), [1] interpolate_cM_chrom() (xftsim.struct.GeneticMap method)

K

k (xftsim.arch.CNoiseComponent property), [1] (xftsim.effect.EffectSpec property), [1] k_components (xftsim.index.ComponentIndex attribute) (xftsim.index.ComponentIndex property) k_phenotypes (xftsim.index.ComponentIndex attribute) (xftsim.index.ComponentIndex property) k_relative (xftsim.index.ComponentIndex attribute) (xftsim.index.ComponentIndex property) k_total (xftsim.index.ComponentIndex attribute) (xftsim.index.ComponentIndex property)

keys (xftsim.struct.PhenotypeArray property) kind (xftsim.arch.AggregationComponent attribute), [1] (xftsim.arch.ArchComponent attribute), [1], [2], [3] (xftsim.arch.CNoiseComponent attribute), [1] (xftsim.arch.GeneticComponent attribute), [1] (xftsim.arch.HaplotypeGeneticComponent attribute), [1] (xftsim.arch.NoiseComponent attribute), [1] (xftsim.arch.ThresholdComponent attribute)

L

LinearAssortativeMating (class in xftsim.mate), [1] load_architecture() (in module xftsim.io) load_effects_npz() (in module xftsim.io)

load_grg() (in module xftsim.io) load_haplotypes_npz() (in module xftsim.io) load_phenotypes_npz() (in module xftsim.io) load_simulation_checkpoint() (in module xftsim.io)

M

m (xftsim.effect.EffectSpec property), [1] (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) (xftsim.index.HaploidVariantIndex attribute) (xftsim.struct.DenseHaplotypeArray property) (xftsim.struct.GraphHaplotypeOperator property) (xftsim.struct.HaplotypeArrayAccessor property) (xftsim.struct.HaplotypeOperator property) (xftsim.struct.StandardizedHaplotypeOperator property) (xftsim.struct.VariantMeta attribute) (xftsim.struct.VariantMeta property) m_causal (xftsim.effect.EffectSpec property), [1] maf (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) (xftsim.index.HaploidVariantIndex attribute) main() (in module xftsim.cli) match() (in module xftsim.utils) matching_indices_conditional() (in module xftsim.utils) mate() (xftsim.mate.BatchedMating method), [1] (xftsim.mate.GeneralAssortativeMating method), [1] (xftsim.mate.LinearAssortativeMating method), [1] (xftsim.mate.RandomMating method), [1] MateAssignment (class in xftsim.mate), [1] maternal_idx (xftsim.mate.MateAssignment attribute), [1] (xftsim.struct.PedigreeArray attribute) MatingStatistics (class in xftsim.stats), [1] matvec() (xftsim.struct.DenseHaplotypeArray method) (xftsim.struct.GraphHaplotypeOperator method) (xftsim.struct.HaplotypeOperator method) (xftsim.struct.StandardizedHaplotypeOperator method) matvec_maternal() (xftsim.struct.DenseHaplotypeArray method) (xftsim.struct.GraphHaplotypeOperator method) (xftsim.struct.HaplotypeOperator method) (xftsim.struct.StandardizedHaplotypeOperator method)

matvec_paternal() (xftsim.struct.DenseHaplotypeArray method) (xftsim.struct.GraphHaplotypeOperator method) (xftsim.struct.HaplotypeOperator method) (xftsim.struct.StandardizedHaplotypeOperator method) means (xftsim.struct.StandardizedHaplotypeOperator property) meiosis() (in module xftsim.reproduce) (xftsim.struct.DenseHaplotypeArray method) (xftsim.struct.GraphHaplotypeOperator method) (xftsim.struct.HaplotypeOperator method) (xftsim.struct.StandardizedHaplotypeOperator method) merge() (xftsim.index.XftIndex method) merge_duplicate_pairs() (in module xftsim.utils) merge_duplicates() (in module xftsim.utils) MixtureCount (class in xftsim.utils) module xftsim.arch xftsim.cli xftsim.effect, [1] xftsim.filters xftsim.founders xftsim.gwas xftsim.index xftsim.io xftsim.mate, [1] xftsim.parser xftsim.ped xftsim.reproduce xftsim.sim, [1] xftsim.stats, [1] xftsim.struct xftsim.utils mother_phenotypes (xftsim.filters.TrioView attribute) MotherComponent (class in xftsim.arch), [1] MultivariateEffects (class in xftsim.effect), [1] MVGeneticComponent (class in xftsim.arch), [1]

N

n (xftsim.gwas.GWASResult attribute), [1] (xftsim.index.SampleIndex attribute) (xftsim.index.SampleIndex property) (xftsim.struct.DenseHaplotypeArray property) (xftsim.struct.GraphHaplotypeOperator property) (xftsim.struct.HaplotypeArrayAccessor property) (xftsim.struct.HaplotypeOperator property) (xftsim.struct.SampleMeta attribute) (xftsim.struct.SampleMeta property) (xftsim.struct.StandardizedHaplotypeOperator property) n_annotations (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) (xftsim.index.HaploidVariantIndex attribute) n_chrom (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) (xftsim.index.HaploidVariantIndex attribute) n_fam (xftsim.index.SampleIndex attribute) (xftsim.index.SampleIndex property) (xftsim.struct.DenseHaplotypeArray property) (xftsim.struct.SampleMeta attribute) (xftsim.struct.SampleMeta property) n_female (xftsim.index.SampleIndex attribute) (xftsim.index.SampleIndex property) (xftsim.struct.DenseHaplotypeArray property) (xftsim.struct.SampleMeta attribute) (xftsim.struct.SampleMeta property) n_male (xftsim.index.SampleIndex attribute) (xftsim.index.SampleIndex property) (xftsim.struct.DenseHaplotypeArray property) (xftsim.struct.SampleMeta attribute) (xftsim.struct.SampleMeta property) n_offspring (xftsim.mate.MateAssignment property), [1] n_pairs (xftsim.filters.SibPairView attribute)

n_subsample (xftsim.filters.SubsampleView attribute), [1] n_trios (xftsim.filters.TrioView attribute) name (xftsim.arch.AggregationComponent attribute), [1] (xftsim.arch.ArchComponent attribute), [1], [2], [3] (xftsim.arch.CNoiseComponent attribute), [1] (xftsim.arch.FatherComponent attribute), [1] (xftsim.arch.GeneticComponent attribute), [1] (xftsim.arch.HaplotypeGeneticComponent attribute), [1] (xftsim.arch.MotherComponent attribute), [1] (xftsim.arch.MVGeneticComponent attribute), [1] (xftsim.arch.NoiseComponent attribute), [1] (xftsim.arch.ParentComponent attribute), [1] (xftsim.arch.SiblingAnyComponent attribute), [1] (xftsim.arch.SiblingCountComponent attribute), [1] (xftsim.arch.SiblingEldestComponent attribute), [1] (xftsim.arch.SiblingMeanComponent attribute), [1] (xftsim.arch.SiblingSumComponent attribute), [1] (xftsim.arch.SiblingYoungestComponent attribute), [1] (xftsim.arch.ThresholdComponent attribute) NegativeBinomialCount (class in xftsim.utils) nodes (xftsim.arch.Architecture property), [1] NoiseComponent (class in xftsim.arch), [1] None() (xftsim.utils.VariableCount method) nonzero_fraction (xftsim.utils.ConstantCount attribute) (xftsim.utils.MixtureCount attribute) (xftsim.utils.NegativeBinomialCount attribute) (xftsim.utils.PoissonCount attribute) (xftsim.utils.VariableCount attribute) (xftsim.utils.VariableCount property) (xftsim.utils.ZeroTruncatedPoissonCount attribute) normalize (xftsim.arch.FatherComponent attribute) (xftsim.arch.MotherComponent attribute) (xftsim.arch.ParentComponent attribute) NullFilter (class in xftsim.index)

O

offspring_phenotypes (xftsim.filters.TrioView attribute) offspring_samples (xftsim.mate.MateAssignment attribute), [1] (xftsim.struct.PedigreeArray attribute) one_allele (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) (xftsim.index.HaploidVariantIndex attribute) (xftsim.struct.VariantMeta attribute)

outputs (xftsim.arch.ArchNode attribute), [1]

P

p_value (xftsim.gwas.GWASResult attribute), [1] parent_n (xftsim.struct.PedigreeArray attribute) ParentComponent (class in xftsim.arch), [1] ParentOffspringRegression (class in xftsim.stats), [1] parse_formula() (in module xftsim.parser) paste() (in module xftsim.utils) paternal_idx (xftsim.mate.MateAssignment attribute), [1] (xftsim.struct.PedigreeArray attribute) Pedigree (class in xftsim.ped) pedigree_history (xftsim.sim.Simulation attribute), [1] PedigreeArray (class in xftsim.struct) PGS (class in xftsim.gwas) phenotype_history (xftsim.sim.Simulation attribute), [1] phenotype_name (xftsim.arch.FatherComponent attribute) (xftsim.arch.MotherComponent attribute) (xftsim.arch.ParentComponent attribute) (xftsim.index.ComponentIndex attribute) (xftsim.index.ComponentIndex property) PhenotypeArray (class in xftsim.struct) phenotypes (xftsim.filters.AscertainedView attribute), [1] (xftsim.filters.SubsampleView attribute), [1] (xftsim.filters.UnrelatedView attribute), [1] (xftsim.sim.Simulation property), [1]

plink1_sample_index() (in module xftsim.io) plink1_variant_index() (in module xftsim.io) ploidy (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) (xftsim.index.HaploidVariantIndex attribute) (xftsim.index.HaploidVariantIndex property) PoissonCount (class in xftsim.utils) pos_bp (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) (xftsim.index.HaploidVariantIndex attribute) (xftsim.struct.DenseHaplotypeArray property) (xftsim.struct.VariantMeta attribute) pos_cM (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) (xftsim.index.HaploidVariantIndex attribute) (xftsim.struct.DenseHaplotypeArray property) (xftsim.struct.VariantMeta attribute) print_tree() (in module xftsim.utils) profiled() (in module xftsim.utils)

R

RandomMating (class in xftsim.mate), [1] RandomSiblingFilter (class in xftsim.index) RandomSiblingSubsampleFilter (class in xftsim.index) RandomSubsampleFilter (class in xftsim.index) range_index() (xftsim.index.ComponentIndex method) (xftsim.index.ComponentIndex static method) read_plink1_as_pseudohaplotypes() (in module xftsim.io) RecombinationMap (class in xftsim.reproduce) recompute_af() (xftsim.struct.DenseHaplotypeArray method) (xftsim.struct.GraphHaplotypeOperator method) (xftsim.struct.HaplotypeOperator method) (xftsim.struct.StandardizedHaplotypeOperator method)

reduce_merge() (xftsim.index.XftIndex static method) results (xftsim.sim.Simulation attribute), [1] resume() (in module xftsim.cli) rmatvec() (xftsim.struct.DenseHaplotypeArray method) (xftsim.struct.GraphHaplotypeOperator method) (xftsim.struct.HaplotypeOperator method) (xftsim.struct.StandardizedHaplotypeOperator method) run() (in module xftsim.cli) (xftsim.gwas.GWAS method) (xftsim.sim.Simulation method), [1]

S

SampleFilter (class in xftsim.index) SampleIndex (class in xftsim.index) sampleIndex_from_plink() (in module xftsim.index) sampleIndex_from_VCF() (in module xftsim.index) SampleMeta (class in xftsim.struct) samples (xftsim.struct.HaplotypeArrayAccessor property) (xftsim.struct.HaplotypeOperator attribute) (xftsim.struct.StandardizedHaplotypeOperator property) SampleStatistics (class in xftsim.stats), [1] save_architecture() (in module xftsim.io) save_effects_npz() (in module xftsim.io) save_haplotypes_npz() (in module xftsim.io) save_phenotypes_npz() (in module xftsim.io) save_simulation_checkpoint() (in module xftsim.io) score() (xftsim.gwas.PGS method) se (xftsim.gwas.GWASResult attribute), [1] sex (xftsim.index.SampleIndex attribute) (xftsim.index.SampleIndex property) (xftsim.struct.DenseHaplotypeArray property) (xftsim.struct.SampleMeta attribute) shape (xftsim.struct.DenseHaplotypeArray property) sib1_idx (xftsim.filters.SibPairView attribute) sib1_phenotypes (xftsim.filters.SibPairView attribute) sib2_idx (xftsim.filters.SibPairView attribute) sib2_phenotypes (xftsim.filters.SibPairView attribute) SiblingAnyComponent (class in xftsim.arch), [1] SiblingCountComponent (class in xftsim.arch), [1] SiblingEldestComponent (class in xftsim.arch), [1] SiblingMeanComponent (class in xftsim.arch), [1]

SiblingPairFilter (class in xftsim.index) SiblingSumComponent (class in xftsim.arch), [1] SiblingYoungestComponent (class in xftsim.arch), [1] SibPairFilter (class in xftsim.filters) SibPairView (class in xftsim.filters) Simulation (class in xftsim.sim), [1] sort_and_paste() (in module xftsim.utils) SparseEffects (class in xftsim.effect), [1] stack() (xftsim.index.XftIndex method) standardize_array() (in module xftsim.utils) standardize_array_hw() (in module xftsim.utils) standardized (xftsim.effect.EffectSpec attribute), [1] standardized_haploid_matvec() (xftsim.struct.DenseHaplotypeArray method) standardized_matvec() (xftsim.struct.DenseHaplotypeArray method) (xftsim.struct.GraphHaplotypeOperator method) (xftsim.struct.HaplotypeOperator method) (xftsim.struct.StandardizedHaplotypeOperator method) standardized_rmatvec() (xftsim.struct.DenseHaplotypeArray method) StandardizedHaplotypeOperator (class in xftsim.struct) Statistic (class in xftsim.stats), [1] statistics (xftsim.stats.GenerationResult attribute), [1] stds (xftsim.struct.StandardizedHaplotypeOperator property) stop (xftsim.sim.Simulation attribute), [1] SubsampleFilter (class in xftsim.filters) SubsampleView (class in xftsim.filters) subset() (xftsim.struct.DenseHaplotypeArray method) (xftsim.struct.PhenotypeArray method) (xftsim.struct.SampleMeta method) (xftsim.struct.VariantMeta method)

T

t_stat (xftsim.gwas.GWASResult attribute), [1] threshold (xftsim.filters.AscertainedView attribute), [1] ThresholdComponent (class in xftsim.arch) to_dense() (xftsim.struct.DenseHaplotypeArray method) (xftsim.struct.GraphHaplotypeOperator method) (xftsim.struct.HaplotypeOperator method) (xftsim.struct.StandardizedHaplotypeOperator method) to_diploid() (xftsim.index.HaploidVariantIndex method), [1] (xftsim.struct.HaplotypeArrayAccessor method) to_diploid_standardized() (xftsim.struct.DenseHaplotypeArray method) (xftsim.struct.HaplotypeArrayAccessor method)

to_haploid() (xftsim.index.ComponentIndex method) (xftsim.index.DiploidVariantIndex method) to_proband() (xftsim.index.ComponentIndex method), [1] to_proportions() (in module xftsim.utils) to_sample_index() (xftsim.struct.SampleMeta method) to_simplex() (in module xftsim.utils) to_variant_index() (xftsim.struct.VariantMeta method) to_vorigin() (xftsim.index.ComponentIndex method), [1] TrioFilter (class in xftsim.filters) TrioView (class in xftsim.filters)

U

unique_identifier (xftsim.index.ComponentIndex attribute) (xftsim.index.ComponentIndex property) (xftsim.index.SampleIndex property) (xftsim.index.XftIndex property) (xftsim.struct.SampleMeta property)

unique_identifier() (in module xftsim.utils) UnrelatedFilter (class in xftsim.filters) UnrelatedView (class in xftsim.filters)

V

validate() (xftsim.index.XftIndex method) values (xftsim.struct.DenseHaplotypeArray property) VariableCount (class in xftsim.utils) variant_mask (xftsim.effect.EffectSpec attribute), [1] variantIndex_from_plink() (in module xftsim.index) variantIndex_from_VCF() (in module xftsim.index) VariantMeta (class in xftsim.struct) variants (xftsim.struct.HaplotypeArrayAccessor property) (xftsim.struct.HaplotypeOperator attribute) (xftsim.struct.StandardizedHaplotypeOperator property)

vid (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) (xftsim.index.HaploidVariantIndex attribute) (xftsim.struct.DenseHaplotypeArray property) (xftsim.struct.VariantMeta attribute) vorigin_relative (xftsim.index.ComponentIndex attribute) (xftsim.index.ComponentIndex property)

W

with_generation() (xftsim.struct.SampleMeta method)

X

xft (xftsim.struct.DenseHaplotypeArray property) XftIndex (class in xftsim.index) xftsim.arch module xftsim.cli module xftsim.effect module, [1] xftsim.filters module xftsim.founders module xftsim.gwas module xftsim.index module xftsim.io module

xftsim.mate module, [1] xftsim.parser module xftsim.ped module xftsim.reproduce module xftsim.sim module, [1] xftsim.stats module, [1] xftsim.struct module xftsim.utils module

Z

zero_allele (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) (xftsim.index.HaploidVariantIndex attribute) (xftsim.struct.VariantMeta attribute)

ZeroTruncatedPoissonCount (class in xftsim.utils)