Index

A

allele_counts() (in module grapp.util.simple)

allele_frequencies() (in module grapp.util.simple)

C

common_mut_dataframe() (in module grapp.util.simple)

E

eigs() (in module grapp.linalg) exact_hamming_dists() (grapp.nn.NearestNeighborContext method) exact_hamming_dists_by_mutation() (grapp.nn.NearestNeighborContext method)

exact_hamming_dists_by_sample() (grapp.nn.NearestNeighborContext method) export_igd() (in module grapp.util.igd) export_vcf() (in module grapp.util.igd)

F

fast_pairwise_hamming() (grapp.nn.NearestNeighborContext method)

G

get_eig_pcs() (in module grapp.linalg) get_variant_type() (in module grapp.util.simple) grapp module grapp.assoc module grapp.linalg module grapp.nn module grapp.util.filter module

grapp.util.igd module grapp.util.simple module grg (grapp.nn.NearestNeighborContext property) grg_save_freq() (in module grapp.util.filter) grg_save_individuals() (in module grapp.util.filter) grg_save_mut_filter() (in module grapp.util.filter) grg_save_populations() (in module grapp.util.filter) grg_save_range() (in module grapp.util.filter) grg_save_samples() (in module grapp.util.filter)

H

hwe() (in module grapp.util.simple)

hwe_df() (in module grapp.util.simple)

I

igd_to_vcf() (in module grapp.util.igd)

INDELS (grapp.util.simple.VariantType attribute)

L

linear_assoc_covar() (in module grapp.assoc)

linear_assoc_no_covar() (in module grapp.assoc)

M

MatrixSelection (class in grapp.linalg) MNPS (grapp.util.simple.VariantType attribute) module grapp grapp.assoc grapp.linalg grapp.nn grapp.util.filter grapp.util.igd grapp.util.simple

multi_grg_save_mut_filter() (in module grapp.util.filter) MultiSciPyStdXOperator (class in grapp.linalg.ops_scipy) MultiSciPyStdXTXOperator (class in grapp.linalg.ops_scipy) MultiSciPyXOperator (class in grapp.linalg.ops_scipy) MultiSciPyXTXOperator (class in grapp.linalg.ops_scipy) muts_above (grapp.nn.NearestNeighborContext property)

N

NearestNeighborContext (class in grapp.nn)

O

OTHER (grapp.util.simple.VariantType attribute)

P

PCs() (in module grapp.linalg)

R

read_pheno() (in module grapp.assoc)

read_plink_covariates() (in module grapp.assoc)

S

samps_below (grapp.nn.NearestNeighborContext property) SciPyStdXOperator (class in grapp.linalg.ops_scipy) SciPyStdXTXOperator (class in grapp.linalg.ops_scipy) SciPyStdXXTOperator (class in grapp.linalg.ops_scipy) SciPyXOperator (class in grapp.linalg.ops_scipy)

SciPyXTXOperator (class in grapp.linalg.ops_scipy) SciPyXXTOperator (class in grapp.linalg.ops_scipy) site_alleles() (in module grapp.util.simple) SNPS (grapp.util.simple.VariantType attribute) sort_by_eigvalues() (in module grapp.linalg) split_by_ranges() (in module grapp.util.filter)

V

variance() (in module grapp.util.simple)

variants_of_types() (in module grapp.util.simple) VariantType (class in grapp.util.simple)

X

X (grapp.linalg.MatrixSelection attribute)

XT (grapp.linalg.MatrixSelection attribute) XTX (grapp.linalg.MatrixSelection attribute)