Index

A

add() (omicsdata.npz.archive.Archive method) adj_to_anc() (in module omicsdata.tree.adj)

adj_to_parents() (in module omicsdata.tree.adj) Archive (class in omicsdata.npz.archive)

C

CHROM (omicsdata.ssm.constants.Variants_Keys attribute) CLUSTERINGS (omicsdata.tree.columns.NEUTREE_Columns attribute) clusterings (omicsdata.tree.neutree.Neutree attribute) CLUSTERS (omicsdata.ssm.columns.PARAMS_Columns attribute) clusters_to_supervars() (in module omicsdata.ssm.supervariants)

COL_ORDER (omicsdata.ssm.columns.SSM_Columns attribute) compute_partial_parents() (in module omicsdata.tree.parents) convert_all_variants_to_tuples() (in module omicsdata.ssm.supervariants) convert_variant_dict_to_tuple() (in module omicsdata.ssm.supervariants) COUNTS (omicsdata.tree.columns.NEUTREE_Columns attribute) counts (omicsdata.tree.neutree.Neutree attribute)

E

extract_nums() (in module omicsdata.ssm.parse)

extract_vids() (in module omicsdata.ssm.common)

G

GARBAGE (omicsdata.ssm.columns.PARAMS_Columns attribute) (omicsdata.tree.columns.NEUTREE_Columns attribute)

garbage (omicsdata.tree.neutree.Neutree attribute) get() (omicsdata.npz.archive.Archive method) get_mutrel() (omicsdata.npz.archive.Archive method)

H

has() (omicsdata.npz.archive.Archive method)

I

ID (omicsdata.ssm.columns.SSM_Columns attribute) (omicsdata.ssm.constants.Variants_Keys attribute)

id (omicsdata.ssm.supervariants.Variant attribute)

L

load() (in module omicsdata.tree.neutree) load_params() (in module omicsdata.ssm.parse) load_ssm() (in module omicsdata.ssm.parse)

load_ssms_and_params() (in module omicsdata.ssm.parse) LOGSCORES (omicsdata.tree.columns.NEUTREE_Columns attribute) logscores (omicsdata.tree.neutree.Neutree attribute)

M

make_superclusters() (in module omicsdata.ssm.supervariants) make_supervar() (in module omicsdata.ssm.supervariants) module omicsdata omicsdata.npz omicsdata.npz.archive omicsdata.ssm omicsdata.ssm.columns omicsdata.ssm.common omicsdata.ssm.constants omicsdata.ssm.convert omicsdata.ssm.parse omicsdata.ssm.supervariants omicsdata.tree.adj omicsdata.tree.columns omicsdata.tree.neutree omicsdata.tree.parents tree

N

NAME (omicsdata.ssm.columns.SSM_Columns attribute) (omicsdata.ssm.constants.Variants_Keys attribute)

Neutree (class in omicsdata.tree.neutree) NEUTREE_Columns (class in omicsdata.tree.columns)

O

OMEGA_V (omicsdata.ssm.constants.Variants_Keys attribute) omega_v (omicsdata.ssm.supervariants.Variant attribute) omicsdata module omicsdata.npz module omicsdata.npz.archive module omicsdata.ssm module omicsdata.ssm.columns module omicsdata.ssm.common module omicsdata.ssm.constants module

omicsdata.ssm.convert module omicsdata.ssm.parse module omicsdata.ssm.supervariants module omicsdata.tree.adj module omicsdata.tree.columns module omicsdata.tree.neutree module omicsdata.tree.parents module

P

PARAMS_Columns (class in omicsdata.ssm.columns) parents_to_adj() (in module omicsdata.tree.parents)

PHIS (omicsdata.tree.columns.NEUTREE_Columns attribute) phis (omicsdata.tree.neutree.Neutree attribute) POS (omicsdata.ssm.constants.Variants_Keys attribute)

R

REF_READS (omicsdata.ssm.constants.Variants_Keys attribute)

ref_reads (omicsdata.ssm.supervariants.Variant attribute) remove_garbage() (in module omicsdata.ssm.parse)

S

SAMPLES (omicsdata.ssm.columns.PARAMS_Columns attribute) save() (in module omicsdata.tree.neutree) (omicsdata.npz.archive.Archive method) sort_vids() (in module omicsdata.ssm.common) SSM_Columns (class in omicsdata.ssm.columns)

ssm_to_pyclone() (in module omicsdata.ssm.convert) ssm_to_viber() (in module omicsdata.ssm.convert) STRUCTS (omicsdata.tree.columns.NEUTREE_Columns attribute) structs (omicsdata.tree.neutree.Neutree attribute) supervars_to_binom_params() (in module omicsdata.ssm.supervariants)

T

TOTAL_READS (omicsdata.ssm.columns.SSM_Columns attribute) (omicsdata.ssm.constants.Variants_Keys attribute)

total_reads (omicsdata.ssm.supervariants.Variant attribute) tree module

V

VAF (omicsdata.ssm.constants.Variants_Keys attribute) vaf (omicsdata.ssm.supervariants.Variant attribute) VAR_READ_PROB (omicsdata.ssm.columns.SSM_Columns attribute) VAR_READS (omicsdata.ssm.columns.SSM_Columns attribute) (omicsdata.ssm.constants.Variants_Keys attribute)

var_reads (omicsdata.ssm.supervariants.Variant attribute) Variant (class in omicsdata.ssm.supervariants) Variants_Keys (class in omicsdata.ssm.constants)

W

write_params() (in module omicsdata.ssm.parse)

write_ssms() (in module omicsdata.ssm.parse)