Index

A

allele_count() (in module anhima.af) allele_counts() (in module anhima.af) allele_frequencies() (in module anhima.af) allele_frequency() (in module anhima.af) allele_number() (in module anhima.af) allelism() (in module anhima.af) anhima (module) anhima.af (module) anhima.dist (module) anhima.f2 (module) anhima.gt (module) anhima.h5 (module) anhima.io (module)

anhima.ld (module) anhima.loc (module) anhima.mds (module) anhima.pca (module) anhima.ped (module) anhima.sf (module) anhima.sim (module) anhima.tree (module) anhima.util (module) as_012() (in module anhima.gt) as_allele_counts() (in module anhima.gt) as_haplotypes() (in module anhima.gt) as_n_alt() (in module anhima.gt)

B

bionj() (in module anhima.tree) block_apply() (in module anhima.util)

block_compress2d() (in module anhima.util) block_take2d() (in module anhima.util)

C

classical() (in module anhima.mds) color_edges_by_group_majority() (in module anhima.tree) compress_variants() (in module anhima.loc) count_called() (in module anhima.gt) count_diploid_mendelian_error() (in module anhima.ped) count_doubletons() (in module anhima.af) count_genotypes() (in module anhima.gt) count_het() (in module anhima.gt) count_hom() (in module anhima.gt)

count_hom_alt() (in module anhima.gt) count_hom_ref() (in module anhima.gt) count_missing() (in module anhima.gt) count_non_segregating() (in module anhima.af) count_non_variant() (in module anhima.af) count_segregating() (in module anhima.af) count_shared_doubletons() (in module anhima.f2) count_singletons() (in module anhima.af) count_variant() (in module anhima.af)

D

diploid_inheritance() (in module anhima.ped)

diploid_mendelian_error() (in module anhima.ped)

E

evenly_downsample_variants() (in module anhima.loc)

I

impute_inheritance_nearest() (in module anhima.ped) is_called() (in module anhima.gt) is_doubleton() (in module anhima.af) is_het() (in module anhima.gt) is_hom() (in module anhima.gt) is_hom_alt() (in module anhima.gt) is_hom_ref() (in module anhima.gt)

is_missing() (in module anhima.gt) is_non_segregating() (in module anhima.af) is_non_variant() (in module anhima.af) is_segregating() (in module anhima.af) is_singleton() (in module anhima.af) is_variant() (in module anhima.af)

L

ld_prune_pairwise() (in module anhima.ld) load_region() (in module anhima.h5) locate_interval() (in module anhima.loc)

locate_intervals() (in module anhima.loc) locate_position() (in module anhima.loc) locate_positions() (in module anhima.loc)

M

max_allele() (in module anhima.gt)

maximum_likelihood_ancestry() (in module anhima.af)

N

nj() (in module anhima.tree)

normalise_doubleton_counts() (in module anhima.f2)

P

pack_diploid() (in module anhima.gt) pairwise_distance() (in module anhima.dist) pairwise_genotype_ld() (in module anhima.ld) pairwise_ld_decay() (in module anhima.ld) pca() (in module anhima.pca) plot_continuous_calldata() (in module anhima.gt) plot_continuous_calldata_by_sample() (in module anhima.gt) plot_coords() (in module anhima.mds) (in module anhima.pca) plot_diploid_genotypes() (in module anhima.gt) plot_discrete_calldata() (in module anhima.gt) plot_f2_fig() (in module anhima.f2) plot_genotype_counts_by_sample() (in module anhima.gt) plot_genotype_counts_by_variant() (in module anhima.gt) plot_ld_decay_by_distance() (in module anhima.ld) plot_ld_decay_by_separation() (in module anhima.ld)

plot_loadings() (in module anhima.pca) plot_pairwise_distance() (in module anhima.dist) plot_pairwise_ld() (in module anhima.ld) plot_phylo() (in module anhima.tree) plot_shared_doubletons() (in module anhima.f2) plot_site_frequency_spectrum() (in module anhima.sf) plot_total_doubletons() (in module anhima.f2) plot_variance_explained() (in module anhima.pca) plot_variant_locator() (in module anhima.loc) plot_windowed_genotype_counts() (in module anhima.gt) plot_windowed_genotype_density() (in module anhima.gt) plot_windowed_genotype_rate() (in module anhima.gt) plot_windowed_ld() (in module anhima.ld) plot_windowed_variant_counts() (in module anhima.loc) plot_windowed_variant_density() (in module anhima.loc)

Q

query_variants() (in module anhima.loc)

R

randomly_downsample_variants() (in module anhima.loc)

read_tree() (in module anhima.tree)

S

save_tped() (in module anhima.h5) (in module anhima.io) simulate_biallelic_genotypes() (in module anhima.sim) simulate_genotypes_with_ld() (in module anhima.sim) simulate_relatedness() (in module anhima.sim) site_frequency_spectrum() (in module anhima.sf)

site_frequency_spectrum_folded() (in module anhima.sf) site_frequency_spectrum_folded_scaled() (in module anhima.sf) site_frequency_spectrum_scaled() (in module anhima.sf) smacof() (in module anhima.mds)

T

take2d_pointsel() (in module anhima.h5) take_samples() (in module anhima.loc)

take_variants() (in module anhima.loc)

U

unpack_diploid() (in module anhima.gt)

V

view_interval() (in module anhima.loc) view_position() (in module anhima.loc)

view_sample() (in module anhima.loc)

W

windowed_genotype_counts() (in module anhima.gt) windowed_genotype_density() (in module anhima.gt) windowed_genotype_rate() (in module anhima.gt) windowed_ld_decay() (in module anhima.ld)

windowed_statistic() (in module anhima.loc) windowed_variant_counts() (in module anhima.loc) windowed_variant_density() (in module anhima.loc) write_tree() (in module anhima.tree)