Uses of Class
org.monarchinitiative.lirical.core.likelihoodratio.LrWithExplanation

Packages that use LrWithExplanation

Package	Description
org.monarchinitiative.lirical.core.analysis	A high-level representation of LIRICAL analysis.
org.monarchinitiative.lirical.core.likelihoodratio	Package with logic for calculation of likelihood ratios for phenotypic or genotypic test results.

Uses of LrWithExplanation in org.monarchinitiative.lirical.core.analysis

Methods in org.monarchinitiative.lirical.core.analysis that return types with arguments of type LrWithExplanation

Modifier and Type	Method	Description
List<LrWithExplanation>	TestResult.excludedResults()
List<LrWithExplanation>	TestResult.observedResults()

Method parameters in org.monarchinitiative.lirical.core.analysis with type arguments of type LrWithExplanation

Modifier and Type	Method	Description
static TestResult	TestResult.of(org.monarchinitiative.phenol.ontology.data.TermId diseaseId, double pretestProbability, List<LrWithExplanation> observedResults, List<LrWithExplanation> excludedResults, GenotypeLrWithExplanation genotypeLr)

Uses of LrWithExplanation in org.monarchinitiative.lirical.core.likelihoodratio

Methods in org.monarchinitiative.lirical.core.likelihoodratio that return LrWithExplanation

Modifier and Type	Method	Description
LrWithExplanation	LrWithExplanationFactory.create(org.monarchinitiative.phenol.ontology.data.TermId term, LrMatchType matchType, double lr)
LrWithExplanation	LrWithExplanationFactory.create(org.monarchinitiative.phenol.ontology.data.TermId queryTerm, org.monarchinitiative.phenol.ontology.data.TermId matchingTerm, LrMatchType matchType, double lr)
LrWithExplanation	PhenotypeLikelihoodRatio.lrForExcludedTerm(org.monarchinitiative.phenol.ontology.data.TermId queryTid, InducedDiseaseGraph idg)	Calculate and return the likelihood ratio of an EXCLUDED HPO feature tid in an individual with the disease "diseaseId"
LrWithExplanation	PhenotypeLikelihoodRatio.lrForObservedTerm(org.monarchinitiative.phenol.ontology.data.TermId queryTid, InducedDiseaseGraph idg)	Calculate and return the likelihood ratio of observing the HPO feature queryTid in an individual with the disease idg (note that the InducedDiseaseGraph contains information about the annotations of the disease that we use to calculate the likelihood ratios).
static LrWithExplanation	LrWithExplanation.of(org.monarchinitiative.phenol.ontology.data.TermId q, org.monarchinitiative.phenol.ontology.data.TermId m, LrMatchType mt, double lr, String explanation)

Methods in org.monarchinitiative.lirical.core.likelihoodratio with parameters of type LrWithExplanation

Modifier and Type	Method	Description
int	LrWithExplanation.compareTo(LrWithExplanation that)	Sort the LrWithExplanation objects in decreasing order according to likelihood ratio score.