Index

B

build() (PhenotypeDatasetBuilder method)

build_relationship_mask() (HPOHierarchyEngine method)

C

compute_correlation_matrix() (HPOCorrelationAnalyzer method)

compute_synergy_matrix() (SynergyAnalyzer method) CorrelationResult (class in phenosign.analysis.hpo_correlation_analyzer)

D

describe_conditions() (PhenotypeDataset method)

describe_sex() (PhenotypeDataset method)

E

evaluate_pair_synergy() (SynergyAnalyzer method)

F

feature_ids (PhenotypeDataset property)

filter_weak_correlations() (CorrelationResult method) filter_weak_synergy() (SynergyResult method)

G

get_condition() (PhenotypeDataset method) get_id_mapping() (HPOHierarchyEngine method) get_labels() (HPOHierarchyEngine method)

get_pmids() (PhenotypeDataset method) get_variant_condition() (PhenotypeDataset method) gpsea_cohort (PhenotypeDataset attribute)

H

has_disease() (in module phenosign.core.predicates) has_exon_and_variant_effect() (in module phenosign.core.predicates) has_gene() (in module phenosign.core.predicates) has_sex() (in module phenosign.core.predicates)

has_variant_effect() (in module phenosign.core.predicates) hpo (HPOHierarchyEngine property) hpo_data (PhenotypeDataset attribute) HPOCorrelationAnalyzer (class in phenosign.analysis.hpo_correlation_analyzer) HPOHierarchyEngine (class in phenosign.ontology._hpo_hierarchy)

I

individual_ids (PhenotypeDataset property)

L

list_diseases() (PhenotypeDataset method)

list_genes() (PhenotypeDataset method)

M

module phenosign.analysis.hpo_correlation_analyzer phenosign.analysis.synergy_analyzer phenosign.core.builder phenosign.core.dataset phenosign.core.predicates phenosign.ontology._hpo_hierarchy

P

phenopackets (PhenotypeDataset attribute) phenosign.analysis.hpo_correlation_analyzer module phenosign.analysis.synergy_analyzer module phenosign.core.builder module phenosign.core.dataset module

phenosign.core.predicates module phenosign.ontology._hpo_hierarchy module PhenotypeDataset (class in phenosign.core.dataset) PhenotypeDatasetBuilder (class in phenosign.core.builder) plot_correlation_heatmap_with_significance() (CorrelationResult method) plot_synergy_heatmap() (SynergyResult method) propagate() (HPOHierarchyEngine method)

R

results_table (CorrelationResult property) (SynergyResult property)

S

save_correlation_heatmap() (CorrelationResult method) save_correlation_results() (CorrelationResult method) save_synergy_heatmap() (SynergyResult method)

save_synergy_results() (SynergyResult method) SynergyAnalyzer (class in phenosign.analysis.synergy_analyzer) SynergyResult (class in phenosign.analysis.synergy_analyzer)

V

variant_effect_summary() (PhenotypeDataset method)