Index

A | B | C | D | E | F | G | H | I | J | L | M | N | P | Q | R | S | T | U | V | W | X

A

allel (module)
allel.chunked (module)
allel.io (module)
allel.model.chunked (module)
allel.model.dask (module)
allel.model.ndarray (module)
allel.model.util (module)
allel.stats.admixture (module)
allel.stats.decomposition (module)
allel.stats.distance (module)
allel.stats.diversity (module)
allel.stats.fst (module)
allel.stats.hw (module)
allel.stats.ld (module)
allel.stats.mendel (module)
allel.stats.misc (module)
allel.stats.preprocessing (module)
allel.stats.roh (module)
allel.stats.selection (module)
allel.stats.sf (module)
allel.stats.window (module)
allel.util (module)
AlleleCountsArray (class in allel.model.ndarray)
AlleleCountsChunkedArray (class in allel.model.chunked)
AlleleCountsDaskArray (class in allel.model.dask)
allelism() (allel.model.ndarray.AlleleCountsArray method)
amax() (in module allel.chunked.core)
amin() (in module allel.chunked.core)
asum() (in module allel.chunked.core)
average_hudson_fst() (in module allel.stats.fst)
average_patterson_d() (in module allel.stats.admixture)
average_patterson_f3() (in module allel.stats.admixture)
average_patterson_fst() (in module allel.stats.fst)
average_weir_cockerham_fst() (in module allel.stats.fst)

B

bcolz_storage (in module allel.chunked.storage_bcolz)
bcolz_zlib1_storage (in module allel.chunked.storage_bcolz)
bcolzmem_storage (in module allel.chunked.storage_bcolz)
bcolzmem_zlib1_storage (in module allel.chunked.storage_bcolz)
BcolzMemStorage (class in allel.chunked.storage_bcolz)
BcolzStorage (class in allel.chunked.storage_bcolz)
bcolztmp_storage (in module allel.chunked.storage_bcolz)
bcolztmp_zlib1_storage (in module allel.chunked.storage_bcolz)
BcolzTmpStorage (class in allel.chunked.storage_bcolz)
binary_op() (in module allel.chunked.core)

C

CenterScaler (class in allel.stats.preprocessing)
ChunkedArrayWrapper (class in allel.chunked.core)
ChunkedTableWrapper (class in allel.chunked.core)
compress() (allel.model.ndarray.AlleleCountsArray method)
(allel.model.ndarray.GenotypeAlleleCounts method)
(allel.model.ndarray.Genotypes method)
(allel.model.ndarray.HaplotypeArray method)
(in module allel.chunked.core)
compress_table() (in module allel.chunked.core)
concatenate() (allel.model.ndarray.AlleleCountsArray method)
(allel.model.ndarray.GenotypeAlleleCounts method)
(allel.model.ndarray.Genotypes method)
(allel.model.ndarray.HaplotypeArray method)
(in module allel.chunked.core)
concatenate_table() (in module allel.chunked.core)
condensed_coords() (in module allel.stats.distance)
condensed_coords_between() (in module allel.stats.distance)
condensed_coords_within() (in module allel.stats.distance)
copy() (in module allel.chunked.core)
copy_table() (in module allel.chunked.core)
count_alleles() (allel.model.ndarray.GenotypeAlleleCountsArray method)
(allel.model.ndarray.GenotypeArray method)
(allel.model.ndarray.HaplotypeArray method)
count_alleles_subpops() (allel.model.ndarray.GenotypeArray method)
(allel.model.ndarray.HaplotypeArray method)
count_alt() (allel.model.ndarray.HaplotypeArray method)
count_call() (allel.model.ndarray.Genotypes method)
(allel.model.ndarray.HaplotypeArray method)
count_called() (allel.model.ndarray.Genotypes method)
(allel.model.ndarray.HaplotypeArray method)
count_doubleton() (allel.model.ndarray.AlleleCountsArray method)
count_het() (allel.model.ndarray.Genotypes method)
count_hom() (allel.model.ndarray.Genotypes method)
count_hom_alt() (allel.model.ndarray.Genotypes method)
count_hom_ref() (allel.model.ndarray.Genotypes method)
count_missing() (allel.model.ndarray.Genotypes method)
(allel.model.ndarray.HaplotypeArray method)
count_non_segregating() (allel.model.ndarray.AlleleCountsArray method)
count_non_variant() (allel.model.ndarray.AlleleCountsArray method)
count_nonzero() (in module allel.chunked.core)
count_ref() (allel.model.ndarray.HaplotypeArray method)
count_segregating() (allel.model.ndarray.AlleleCountsArray method)
count_singleton() (allel.model.ndarray.AlleleCountsArray method)
count_variant() (allel.model.ndarray.AlleleCountsArray method)
create_allele_mapping() (in module allel.model.util)

D

distinct() (allel.model.ndarray.HaplotypeArray method)
distinct_counts() (allel.model.ndarray.HaplotypeArray method)
distinct_frequencies() (allel.model.ndarray.HaplotypeArray method)

E

ehh_decay() (in module allel.stats.selection)
equally_accessible_windows() (in module allel.stats.window)
eval() (allel.model.ndarray.FeatureTable method)
(allel.model.ndarray.VariantTable method)
eval_table() (in module allel.chunked.core)

F

FeatureChunkedTable (class in allel.model.chunked), [1]
FeatureTable (class in allel.model.ndarray)
fig_voight_painting() (in module allel.stats.selection)
fill_masked() (allel.model.ndarray.Genotypes method)
fold_joint_sfs() (in module allel.stats.sf)
fold_sfs() (in module allel.stats.sf)
from_gff3() (allel.model.ndarray.FeatureTable static method)
from_packed() (allel.model.ndarray.GenotypeArray class method)
from_sparse() (allel.model.ndarray.GenotypeArray static method)
(allel.model.ndarray.HaplotypeArray static method)

G

garud_h() (in module allel.stats.selection)
GenotypeAlleleCounts (class in allel.model.ndarray)
GenotypeAlleleCountsArray (class in allel.model.ndarray)
GenotypeAlleleCountsVector (class in allel.model.ndarray)
GenotypeArray (class in allel.model.ndarray)
GenotypeChunkedArray (class in allel.model.chunked)
GenotypeDaskArray (class in allel.model.dask)
Genotypes (class in allel.model.ndarray)
GenotypeVector (class in allel.model.ndarray)
get_scaler() (in module allel.stats.preprocessing)

H

h5fmem() (in module allel.chunked.storage_hdf5)
h5ftmp() (in module allel.chunked.storage_hdf5)
haploidify_samples() (allel.model.ndarray.GenotypeArray method)
haplotype_diversity() (in module allel.stats.selection)
HaplotypeArray (class in allel.model.ndarray)
HaplotypeChunkedArray (class in allel.model.chunked)
HaplotypeDaskArray (class in allel.model.dask)
hdf5_cache() (in module allel.util)
hdf5_lzf_storage (in module allel.chunked.storage_hdf5)
hdf5_storage (in module allel.chunked.storage_hdf5)
hdf5_zlib1_storage (in module allel.chunked.storage_hdf5)
hdf5mem_lzf_storage (in module allel.chunked.storage_hdf5)
hdf5mem_storage (in module allel.chunked.storage_hdf5)
hdf5mem_zlib1_storage (in module allel.chunked.storage_hdf5)
HDF5MemStorage (class in allel.chunked.storage_hdf5)
HDF5Storage (class in allel.chunked.storage_hdf5)
hdf5tmp_lzf_storage (in module allel.chunked.storage_hdf5)
hdf5tmp_storage (in module allel.chunked.storage_hdf5)
hdf5tmp_zlib1_storage (in module allel.chunked.storage_hdf5)
HDF5TmpStorage (class in allel.chunked.storage_hdf5)
heterozygosity_expected() (in module allel.stats.hw)
heterozygosity_observed() (in module allel.stats.hw)
hudson_fst() (in module allel.stats.fst)

I

ihs() (in module allel.stats.selection)
inbreeding_coefficient() (in module allel.stats.hw)
intersect() (allel.model.ndarray.SortedIndex method)
(allel.model.ndarray.UniqueIndex method)
intersect_range() (allel.model.ndarray.SortedIndex method)
intersect_ranges() (allel.model.ndarray.SortedIndex method)
is_alt() (allel.model.ndarray.HaplotypeArray method)
is_biallelic() (allel.model.ndarray.AlleleCountsArray method)
is_biallelic_01() (allel.model.ndarray.AlleleCountsArray method)
is_call() (allel.model.ndarray.Genotypes method)
(allel.model.ndarray.HaplotypeArray method)
is_called() (allel.model.ndarray.GenotypeAlleleCounts method)
(allel.model.ndarray.Genotypes method)
(allel.model.ndarray.HaplotypeArray method)
is_doubleton() (allel.model.ndarray.AlleleCountsArray method)
is_het() (allel.model.ndarray.GenotypeAlleleCounts method)
(allel.model.ndarray.Genotypes method)
is_hom() (allel.model.ndarray.GenotypeAlleleCounts method)
(allel.model.ndarray.Genotypes method)
is_hom_alt() (allel.model.ndarray.GenotypeAlleleCounts method)
(allel.model.ndarray.Genotypes method)
is_hom_ref() (allel.model.ndarray.GenotypeAlleleCounts method)
(allel.model.ndarray.Genotypes method)
is_missing() (allel.model.ndarray.GenotypeAlleleCounts method)
(allel.model.ndarray.Genotypes method)
(allel.model.ndarray.HaplotypeArray method)
is_non_segregating() (allel.model.ndarray.AlleleCountsArray method)
is_non_variant() (allel.model.ndarray.AlleleCountsArray method)
is_phased (allel.model.ndarray.Genotypes attribute)
is_ref() (allel.model.ndarray.HaplotypeArray method)
is_segregating() (allel.model.ndarray.AlleleCountsArray method)
is_singleton() (allel.model.ndarray.AlleleCountsArray method)
is_unique (allel.model.ndarray.SortedIndex attribute)
is_variant() (allel.model.ndarray.AlleleCountsArray method)
iter_gff3() (in module allel.io)

J

joint_sfs() (in module allel.stats.sf)
joint_sfs_folded() (in module allel.stats.sf)
joint_sfs_folded_scaled() (in module allel.stats.sf)
joint_sfs_scaled() (in module allel.stats.sf)

L

locate_fixed_differences() (in module allel.model.util)
locate_intersection() (allel.model.ndarray.SortedIndex method)
(allel.model.ndarray.UniqueIndex method)
locate_intersection_ranges() (allel.model.ndarray.SortedIndex method)
locate_key() (allel.model.ndarray.SortedIndex method)
(allel.model.ndarray.SortedMultiIndex method)
(allel.model.ndarray.UniqueIndex method)
locate_keys() (allel.model.ndarray.SortedIndex method)
(allel.model.ndarray.UniqueIndex method)
locate_private_alleles() (in module allel.model.util)
locate_range() (allel.model.ndarray.SortedIndex method)
(allel.model.ndarray.SortedMultiIndex method)
locate_ranges() (allel.model.ndarray.SortedIndex method)
locate_unlinked() (in module allel.stats.ld)

M

map_alleles() (allel.model.ndarray.AlleleCountsArray method)
(allel.model.ndarray.Genotypes method)
(allel.model.ndarray.HaplotypeArray method)
map_blocks() (in module allel.chunked.core)
mask (allel.model.ndarray.Genotypes attribute)
max_allele() (allel.model.ndarray.AlleleCountsArray method)
mean_pairwise_difference() (in module allel.stats.diversity)
mean_pairwise_difference_between() (in module allel.stats.diversity)
mendel_errors() (in module allel.stats.mendel)
moving_delta_tajima_d() (in module allel.stats.selection)
moving_garud_h() (in module allel.stats.selection)
moving_haplotype_diversity() (in module allel.stats.selection)
moving_hudson_fst() (in module allel.stats.fst)
moving_patterson_d() (in module allel.stats.admixture)
moving_patterson_f3() (in module allel.stats.admixture)
moving_patterson_fst() (in module allel.stats.fst)
moving_statistic() (in module allel.stats.window)
moving_tajima_d() (in module allel.stats.diversity)
moving_weir_cockerham_fst() (in module allel.stats.fst)

N

n_allele_calls (allel.model.ndarray.GenotypeArray attribute)
(allel.model.ndarray.GenotypeVector attribute)
n_alleles (allel.model.ndarray.AlleleCountsArray attribute)
(allel.model.ndarray.GenotypeAlleleCountsArray attribute)
(allel.model.ndarray.GenotypeAlleleCountsVector attribute)
n_calls (allel.model.ndarray.GenotypeAlleleCountsVector attribute)
(allel.model.ndarray.GenotypeArray attribute)
(allel.model.ndarray.GenotypeVector attribute)
n_features (allel.model.ndarray.FeatureTable attribute)
n_haplotypes (allel.model.ndarray.HaplotypeArray attribute)
n_samples (allel.model.ndarray.GenotypeAlleleCountsArray attribute)
(allel.model.ndarray.GenotypeArray attribute)
n_variants (allel.model.ndarray.AlleleCountsArray attribute)
(allel.model.ndarray.GenotypeAlleleCountsArray attribute)
(allel.model.ndarray.GenotypeArray attribute)
(allel.model.ndarray.HaplotypeArray attribute)
(allel.model.ndarray.VariantTable attribute)
names (allel.model.ndarray.FeatureTable attribute)
(allel.model.ndarray.VariantTable attribute)
nsl() (in module allel.stats.selection)

P

paint_transmission() (in module allel.stats.mendel)
pairwise_distance() (in module allel.stats.distance)
pairwise_dxy() (in module allel.stats.distance)
patterson_d() (in module allel.stats.admixture)
patterson_f2() (in module allel.stats.admixture)
patterson_f3() (in module allel.stats.admixture)
patterson_fst() (in module allel.stats.fst)
PattersonScaler (class in allel.stats.preprocessing)
pca() (in module allel.stats.decomposition)
pcoa() (in module allel.stats.distance)
per_base() (in module allel.stats.window)
phase_by_transmission() (in module allel.stats.mendel)
phase_parents_by_transmission() (in module allel.stats.mendel)
phase_progeny_by_transmission() (in module allel.stats.mendel)
ploidy (allel.model.ndarray.GenotypeArray attribute)
(allel.model.ndarray.GenotypeVector attribute)
plot_haplotype_frequencies() (in module allel.stats.selection)
plot_joint_sfs() (in module allel.stats.sf)
plot_joint_sfs_folded() (in module allel.stats.sf)
plot_joint_sfs_folded_scaled() (in module allel.stats.sf)
plot_joint_sfs_scaled() (in module allel.stats.sf)
plot_moving_haplotype_frequencies() (in module allel.stats.selection)
plot_pairwise_distance() (in module allel.stats.distance)
plot_pairwise_ld() (in module allel.stats.ld)
plot_sfs() (in module allel.stats.sf)
plot_sfs_folded() (in module allel.stats.sf)
plot_sfs_folded_scaled() (in module allel.stats.sf)
plot_sfs_scaled() (in module allel.stats.sf)
plot_variant_locator() (in module allel.stats.misc)
plot_voight_painting() (in module allel.stats.selection)
prefix_argsort() (allel.model.ndarray.HaplotypeArray method)

Q

query() (allel.model.ndarray.FeatureTable method)
(allel.model.ndarray.VariantTable method)
query_position() (allel.model.ndarray.VariantTable method)
query_region() (allel.model.ndarray.VariantTable method)

R

randomized_pca() (in module allel.stats.decomposition)
reduce_axis() (in module allel.chunked.core)
rogers_huff_r() (in module allel.stats.ld)
rogers_huff_r_between() (in module allel.stats.ld)
roh_mhmm() (in module allel.stats.roh)

S

sample_to_haplotype_selection() (in module allel.model.util)
scale_joint_sfs() (in module allel.stats.sf)
scale_joint_sfs_folded() (in module allel.stats.sf)
scale_sfs() (in module allel.stats.sf)
scale_sfs_folded() (in module allel.stats.sf)
sequence_divergence() (in module allel.stats.diversity)
sequence_diversity() (in module allel.stats.diversity)
sfs() (in module allel.stats.sf)
sfs_folded() (in module allel.stats.sf)
sfs_folded_scaled() (in module allel.stats.sf)
sfs_scaled() (in module allel.stats.sf)
SortedIndex (class in allel.model.ndarray)
SortedMultiIndex (class in allel.model.ndarray)
standardize() (in module allel.stats.selection)
standardize_by_allele_count() (in module allel.stats.selection)
StandardScaler (class in allel.stats.preprocessing)
store() (in module allel.chunked.core)
subset() (allel.model.ndarray.GenotypeAlleleCountsArray method)
(allel.model.ndarray.GenotypeArray method)
(allel.model.ndarray.HaplotypeArray method), [1]
(in module allel.chunked.core)

T

tabulate_state_blocks() (in module allel.stats.misc)
tabulate_state_transitions() (in module allel.stats.misc)
tajima_d() (in module allel.stats.diversity)
take() (allel.model.ndarray.AlleleCountsArray method)
(allel.model.ndarray.GenotypeAlleleCounts method)
(allel.model.ndarray.Genotypes method)
(allel.model.ndarray.HaplotypeArray method)
(in module allel.chunked.core)
take_table() (in module allel.chunked.core)
to_allele_counts() (allel.model.ndarray.Genotypes method)
to_frequencies() (allel.model.ndarray.AlleleCountsArray method)
to_genotypes() (allel.model.ndarray.HaplotypeArray method)
to_gt() (allel.model.ndarray.Genotypes method)
to_mask() (allel.model.ndarray.FeatureTable method)
to_n_alt() (allel.model.ndarray.Genotypes method)
to_n_ref() (allel.model.ndarray.Genotypes method)
to_packed() (allel.model.ndarray.GenotypeArray method)
to_sparse() (allel.model.ndarray.GenotypeArray method)
(allel.model.ndarray.HaplotypeArray method)
to_vcf() (allel.model.ndarray.VariantTable method)

U

UniqueIndex (class in allel.model.ndarray)

V

VariantChunkedTable (class in allel.model.chunked)
VariantTable (class in allel.model.ndarray)
voight_painting() (in module allel.stats.selection)

W

watterson_theta() (in module allel.stats.diversity)
weir_cockerham_fst() (in module allel.stats.fst)
windowed_count() (in module allel.stats.window)
windowed_df() (in module allel.stats.diversity)
windowed_divergence() (in module allel.stats.diversity)
windowed_diversity() (in module allel.stats.diversity)
windowed_hudson_fst() (in module allel.stats.fst)
windowed_patterson_fst() (in module allel.stats.fst)
windowed_r_squared() (in module allel.stats.ld)
windowed_statistic() (in module allel.stats.window)
windowed_tajima_d() (in module allel.stats.diversity)
windowed_watterson_theta() (in module allel.stats.diversity)
windowed_weir_cockerham_fst() (in module allel.stats.fst)
write_fasta() (in module allel.io)
write_vcf() (in module allel.io)

X

xpehh() (in module allel.stats.selection)
xpnsl() (in module allel.stats.selection)