Package org.monarchinitiative.lirical.core.likelihoodratio

Class InducedDiseaseGraph

java.lang.Object

org.monarchinitiative.lirical.core.likelihoodratio.InducedDiseaseGraph

public class InducedDiseaseGraph
extends Object

For some calculations of the phenotype likelihood ratio, we need to traverse the graph induced by the HPO terms to which a disease is annotated. It is cheaper to create this graph once and reuse it for each of the query terms. This class organizes that calculation. Note that this class is only used if there are no direct matches, so there is no need to store the directly annotated diseases here.

Author:

Peter Robinson

Method Summary

Modifier and Type	Method	Description
static InducedDiseaseGraph	create(org.monarchinitiative.phenol.annotations.formats.hpo.HpoDisease disease, org.monarchinitiative.phenol.ontology.data.MinimalOntology ontology)
org.monarchinitiative.phenol.annotations.formats.hpo.HpoDisease	getDisease()
boolean	isExactExcludedMatch(org.monarchinitiative.phenol.ontology.data.TermId tid)	See comments about inducedNegativeGraph.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Details

create

public static InducedDiseaseGraph create(org.monarchinitiative.phenol.annotations.formats.hpo.HpoDisease disease,
 org.monarchinitiative.phenol.ontology.data.MinimalOntology ontology)

isExactExcludedMatch

public boolean isExactExcludedMatch(org.monarchinitiative.phenol.ontology.data.TermId tid)

See comments about inducedNegativeGraph.

Parameters:

tid - A term that was negated in a patient

Returns:

true if the term is also negated in the disease.

getDisease

public org.monarchinitiative.phenol.annotations.formats.hpo.HpoDisease getDisease()