Index

A

accessible_mask (pg_gpu.GenotypeMatrix property) (pg_gpu.HaplotypeMatrix property) align_bp (pg_gpu.streaming_matrix.StreamingGenotypeMatrix property) (pg_gpu.streaming_matrix.StreamingHaplotypeMatrix property) all_tests() (pg_gpu.diversity.FrequencySpectrum method) all_thetas() (pg_gpu.diversity.FrequencySpectrum method)

allel_zarr_to_vcz() (in module pg_gpu.zarr_io) allele_frequency_spectrum() (in module pg_gpu.diversity) (pg_gpu.HaplotypeMatrix method) apply_biallelic_filter() (pg_gpu.GenotypeMatrix method) (pg_gpu.HaplotypeMatrix method) average_patterson_d() (in module pg_gpu.admixture) average_patterson_f3() (in module pg_gpu.admixture)

B

block_bootstrap() (in module pg_gpu.resampling)

block_jackknife() (in module pg_gpu.resampling)

C

chrom (pg_gpu.zarr_source.ZarrGenotypeSource attribute) chrom_end (pg_gpu.streaming_matrix.StreamingGenotypeMatrix property) (pg_gpu.streaming_matrix.StreamingHaplotypeMatrix property) chrom_start (pg_gpu.streaming_matrix.StreamingGenotypeMatrix property) (pg_gpu.streaming_matrix.StreamingHaplotypeMatrix property) chunks (pg_gpu.zarr_source.ZarrGenotypeSource attribute) close() (pg_gpu.streaming_matrix.KvikioChunkFetcher method)

compute_ld_statistics() (in module pg_gpu.ld_statistics) (in module pg_gpu.moments_ld) compute_ld_statistics_gpu_single_pop() (pg_gpu.HaplotypeMatrix method) compute_ld_statistics_gpu_two_pops() (pg_gpu.HaplotypeMatrix method) corner_indices (pg_gpu.decomposition.LostructResult attribute) corners() (in module pg_gpu.decomposition) count_called() (pg_gpu.HaplotypeMatrix method) count_missing() (pg_gpu.HaplotypeMatrix method)

D

da() (in module pg_gpu.divergence) daf_histogram() (in module pg_gpu.diversity) dd() (in module pg_gpu.divergence) (in module pg_gpu.ld_statistics) dd_between() (in module pg_gpu.ld_statistics) dd_rank() (in module pg_gpu.divergence) dd_within() (in module pg_gpu.ld_statistics) device (pg_gpu.GenotypeMatrix property) (pg_gpu.HaplotypeMatrix property) diplotype_frequency_spectrum() (in module pg_gpu.diversity) dist_kurt() (in module pg_gpu.distance_stats)

dist_moments() (in module pg_gpu.distance_stats) dist_skew() (in module pg_gpu.distance_stats) dist_var() (in module pg_gpu.distance_stats) distance (pg_gpu.decomposition.LostructResult attribute) distance_based_stats() (in module pg_gpu.divergence) divergence_stats() (in module pg_gpu.divergence) diversity() (pg_gpu.HaplotypeMatrix method) diversity_stats() (in module pg_gpu.diversity) dxy() (in module pg_gpu.divergence) dxy_min() (in module pg_gpu.divergence) dz() (in module pg_gpu.ld_statistics)

E

ehh_decay() (in module pg_gpu.selection) eigvals (pg_gpu.decomposition.LocalPCAResult attribute)

eigvecs (pg_gpu.decomposition.LocalPCAResult attribute) exclude_missing_sites() (pg_gpu.HaplotypeMatrix method) explained_variance_ratio (pg_gpu.decomposition.LostructResult attribute)

F

fay_wu_h() (pg_gpu.diversity.FrequencySpectrum method) fay_wus_h() (in module pg_gpu.diversity) filter() (pg_gpu.GenotypeMatrix method) (pg_gpu.HaplotypeMatrix method) filter_variants_by_missing() (pg_gpu.HaplotypeMatrix method) fold_joint_sfs() (in module pg_gpu.sfs) fold_sfs() (in module pg_gpu.sfs) FrequencySpectrum (class in pg_gpu.diversity) from_haplotype_matrix() (pg_gpu.GenotypeMatrix class method)

from_ts() (pg_gpu.HaplotypeMatrix class method) from_vcf() (pg_gpu.GenotypeMatrix class method) (pg_gpu.HaplotypeMatrix class method) from_zarr() (pg_gpu.GenotypeMatrix class method) (pg_gpu.HaplotypeMatrix class method) fst() (in module pg_gpu.divergence) fst_hudson() (in module pg_gpu.divergence) fst_nei() (in module pg_gpu.divergence) fst_weir_cockerham() (in module pg_gpu.divergence)

G

garud_h() (in module pg_gpu.selection) GenotypeMatrix (class in pg_gpu) genotypes (pg_gpu.GenotypeMatrix property) get_matrix() (pg_gpu.HaplotypeMatrix method) get_positions() (pg_gpu.HaplotypeMatrix method)

get_span() (pg_gpu.HaplotypeMatrix method) get_subset() (pg_gpu.HaplotypeMatrix method) get_subset_from_range() (pg_gpu.HaplotypeMatrix method) gmin() (in module pg_gpu.divergence) grm() (in module pg_gpu.relatedness)

H

haplotype_count() (in module pg_gpu.diversity) haplotype_diversity() (in module pg_gpu.diversity) HaplotypeMatrix (class in pg_gpu) haplotypes (pg_gpu.HaplotypeMatrix property) has_accessible_mask (pg_gpu.GenotypeMatrix property) (pg_gpu.HaplotypeMatrix property)

has_invariant_info (pg_gpu.GenotypeMatrix property) (pg_gpu.HaplotypeMatrix property) heterozygosity_expected() (in module pg_gpu.diversity) heterozygosity_observed() (in module pg_gpu.diversity) HostChunkFetcher (class in pg_gpu.streaming_matrix)

I

ibs() (in module pg_gpu.relatedness) ihs() (in module pg_gpu.selection) inbreeding_coefficient() (in module pg_gpu.diversity) is_called() (pg_gpu.HaplotypeMatrix method) is_missing() (pg_gpu.HaplotypeMatrix method)

iter_chunks() (pg_gpu.streaming_matrix.HostChunkFetcher method) (pg_gpu.streaming_matrix.KvikioChunkFetcher method) (pg_gpu.zarr_source.ZarrGenotypeSource method) iter_gpu_chunks() (pg_gpu.streaming_matrix.StreamingGenotypeMatrix method) (pg_gpu.streaming_matrix.StreamingHaplotypeMatrix method)

J

jackknife_se (pg_gpu.decomposition.LocalPCAResult attribute) joint_sfs() (in module pg_gpu.sfs)

joint_sfs_folded() (in module pg_gpu.sfs) joint_sfs_folded_scaled() (in module pg_gpu.sfs) joint_sfs_scaled() (in module pg_gpu.sfs)

K

k (pg_gpu.decomposition.LocalPCAResult attribute)

KvikioChunkFetcher (class in pg_gpu.streaming_matrix)

L

load_pop_file() (pg_gpu.GenotypeMatrix method) (pg_gpu.HaplotypeMatrix method) local_pca (pg_gpu.decomposition.LostructResult attribute) local_pca() (in module pg_gpu.decomposition)

local_pca_jackknife() (in module pg_gpu.decomposition) LocalPCAResult (class in pg_gpu.decomposition) locate_unlinked() (pg_gpu.HaplotypeMatrix method) lostruct() (in module pg_gpu.decomposition) LostructResult (class in pg_gpu.decomposition)

M

materialize() (pg_gpu.streaming_matrix.StreamingGenotypeMatrix method) (pg_gpu.streaming_matrix.StreamingHaplotypeMatrix method) max_daf() (in module pg_gpu.diversity) mds (pg_gpu.decomposition.LostructResult attribute) MemoryLimitedWarning (class in pg_gpu) missing_data (pg_gpu.decomposition.LocalPCAResult attribute)

moving_garud_h() (in module pg_gpu.selection) moving_patterson_d() (in module pg_gpu.admixture) moving_patterson_f3() (in module pg_gpu.admixture) mu_ld() (in module pg_gpu.ld_statistics) mu_sfs() (in module pg_gpu.diversity) mu_var() (in module pg_gpu.diversity)

N

n_callable_sites (pg_gpu.GenotypeMatrix property) (pg_gpu.HaplotypeMatrix property) n_invariant_sites (pg_gpu.GenotypeMatrix property) (pg_gpu.HaplotypeMatrix property) n_segregating_sites (pg_gpu.GenotypeMatrix property) (pg_gpu.HaplotypeMatrix property) neutrality_test() (pg_gpu.diversity.FrequencySpectrum method) neutrality_tests() (in module pg_gpu.diversity)

normalized_fay_wus_h() (in module pg_gpu.diversity) nsl() (in module pg_gpu.selection) num_diploids (pg_gpu.zarr_source.ZarrGenotypeSource attribute) num_haplotypes (pg_gpu.HaplotypeMatrix property) (pg_gpu.zarr_source.ZarrGenotypeSource attribute) num_individuals (pg_gpu.GenotypeMatrix property) num_variants (pg_gpu.GenotypeMatrix property) (pg_gpu.HaplotypeMatrix property) (pg_gpu.zarr_source.ZarrGenotypeSource attribute)

O

omega() (in module pg_gpu.ld_statistics)

P

pairwise_diffs() (in module pg_gpu.distance_stats) pairwise_distance() (in module pg_gpu.decomposition) pairwise_distance_matrix() (in module pg_gpu.divergence) pairwise_fst() (in module pg_gpu.divergence) pairwise_LD_v() (pg_gpu.HaplotypeMatrix method) pairwise_r2() (pg_gpu.HaplotypeMatrix method) patterson_d() (in module pg_gpu.admixture) patterson_f2() (in module pg_gpu.admixture) patterson_f3() (in module pg_gpu.admixture) pbs() (in module pg_gpu.divergence) pc_dist() (in module pg_gpu.decomposition) pca() (in module pg_gpu.decomposition) pcoa() (in module pg_gpu.decomposition) pi() (in module pg_gpu.diversity) pi2() (in module pg_gpu.ld_statistics)

plot_haplotype_frequencies() (in module pg_gpu.plotting) plot_joint_sfs() (in module pg_gpu.plotting) plot_ld_decay() (in module pg_gpu.plotting) plot_pairwise_distance() (in module pg_gpu.plotting) plot_pairwise_ld() (in module pg_gpu.plotting) plot_pca() (in module pg_gpu.plotting) plot_sfs() (in module pg_gpu.plotting) plot_variant_locator() (in module pg_gpu.plotting) plot_windowed() (in module pg_gpu.plotting) plot_windowed_panel() (in module pg_gpu.plotting) pop_cols (pg_gpu.zarr_source.ZarrGenotypeSource attribute) positions (pg_gpu.GenotypeMatrix property) (pg_gpu.HaplotypeMatrix property) project() (pg_gpu.diversity.FrequencySpectrum method) project_joint_sfs() (in module pg_gpu.sfs)

R

r() (in module pg_gpu.ld_statistics) r_squared() (in module pg_gpu.ld_statistics)

randomized_pca() (in module pg_gpu.decomposition) remove_accessible_mask() (pg_gpu.GenotypeMatrix method) (pg_gpu.HaplotypeMatrix method)

S

sample_sets (pg_gpu.GenotypeMatrix property) (pg_gpu.HaplotypeMatrix property) (pg_gpu.streaming_matrix.StreamingGenotypeMatrix property) (pg_gpu.streaming_matrix.StreamingHaplotypeMatrix property) scale_joint_sfs() (in module pg_gpu.sfs) scale_joint_sfs_folded() (in module pg_gpu.sfs) scale_sfs() (in module pg_gpu.sfs) scale_sfs_folded() (in module pg_gpu.sfs) scaler (pg_gpu.decomposition.LocalPCAResult attribute) segregating_sites() (in module pg_gpu.diversity) set_accessible_mask() (pg_gpu.GenotypeMatrix method) (pg_gpu.HaplotypeMatrix method) sfs() (in module pg_gpu.sfs) (pg_gpu.diversity.FrequencySpectrum method) sfs_folded() (in module pg_gpu.sfs) sfs_folded_scaled() (in module pg_gpu.sfs)

sfs_scaled() (in module pg_gpu.sfs) shape (pg_gpu.GenotypeMatrix property) (pg_gpu.HaplotypeMatrix property) singleton_count() (in module pg_gpu.diversity) site_pos (pg_gpu.zarr_source.ZarrGenotypeSource attribute) slice_region() (pg_gpu.zarr_source.ZarrGenotypeSource method) slice_region_gpu() (pg_gpu.zarr_source.ZarrGenotypeSource method) slice_subsample() (pg_gpu.zarr_source.ZarrGenotypeSource method) slice_subsample_gpu() (pg_gpu.zarr_source.ZarrGenotypeSource method) snn() (in module pg_gpu.divergence) standardize() (in module pg_gpu.selection) standardize_by_allele_count() (in module pg_gpu.selection) StreamingGenotypeMatrix (class in pg_gpu.streaming_matrix) StreamingHaplotypeMatrix (class in pg_gpu.streaming_matrix) suggest_projection_n() (pg_gpu.diversity.FrequencySpectrum method) summarize_missing_data() (pg_gpu.HaplotypeMatrix method) sumsq (pg_gpu.decomposition.LocalPCAResult attribute)

T

tajimas_d() (in module pg_gpu.diversity) (pg_gpu.diversity.FrequencySpectrum method) Tajimas_D() (pg_gpu.HaplotypeMatrix method) tally_gpu_haplotypes() (pg_gpu.HaplotypeMatrix method) tally_gpu_haplotypes_two_pops() (pg_gpu.HaplotypeMatrix method) tally_gpu_haplotypes_two_pops_with_missing() (pg_gpu.HaplotypeMatrix method) theta() (pg_gpu.diversity.FrequencySpectrum method) theta_h() (in module pg_gpu.diversity) theta_l() (in module pg_gpu.diversity)

theta_w() (in module pg_gpu.diversity) to_haplotype_matrix() (pg_gpu.GenotypeMatrix method) to_lostruct_matrix() (pg_gpu.decomposition.LocalPCAResult method) to_zarr() (pg_gpu.GenotypeMatrix method) (pg_gpu.HaplotypeMatrix method) transfer_to_cpu() (pg_gpu.GenotypeMatrix method) (pg_gpu.HaplotypeMatrix method) transfer_to_gpu() (pg_gpu.GenotypeMatrix method) (pg_gpu.HaplotypeMatrix method)

V

vcf_to_zarr() (pg_gpu.HaplotypeMatrix static method)

W

watersons_theta() (pg_gpu.HaplotypeMatrix method) windowed_analysis() (in module pg_gpu.windowed_analysis) windowed_r_squared() (pg_gpu.HaplotypeMatrix method)

windowed_statistics() (in module pg_gpu.windowed_analysis) windowed_statistics_fused() (in module pg_gpu.windowed_analysis) windows (pg_gpu.decomposition.LocalPCAResult attribute) (pg_gpu.decomposition.LostructResult property)

X

xpehh() (in module pg_gpu.selection)

xpnsl() (in module pg_gpu.selection)

Z

ZarrGenotypeSource (class in pg_gpu.zarr_source) zeng_dh() (in module pg_gpu.diversity) zeng_e() (in module pg_gpu.diversity) (pg_gpu.diversity.FrequencySpectrum method)

zns() (in module pg_gpu.ld_statistics) zx() (in module pg_gpu.divergence)