Package org.monarchinitiative.lirical.core.likelihoodratio

package org.monarchinitiative.lirical.core.likelihoodratio

Package with logic for calculation of likelihood ratios for phenotypic or genotypic test results.

Author:

Peter Robinson

Related Packages

Package	Description
org.monarchinitiative.lirical.core	Core functionality of the LIRICAL algorithm.
org.monarchinitiative.lirical.core.likelihoodratio.poisson	Classes in this package were slightly adapted from the Apache Math version 3 library and remain under the Apache License, Version 2.0.

Class	Description
GenotypeLikelihoodRatio	This class is responsible for calculating the likelihood ratio for genotypes, as described in the Material and Methods | Likelihood Ratio for Genotypes section of the LIRICAL manuscript.
GenotypeLikelihoodRatio.Options
GenotypeLrMatchType	The enum for representing the type of the genotype likelihood ratio analysis performed for a gene.
GenotypeLrWithExplanation	Results of genotype likelihood ratio evaluation for a single gene.
InducedDiseaseGraph	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.
LrMatchType
LrWithExplanation	There are five possible ways that a query term can match a disease term.
LrWithExplanationFactory
PhenotypeLikelihoodRatio	This class is designed to calculate the background and foreground frequencies of any HPO term in any disease (This is calculated by PhenotypeLikelihoodRatio.initializeFrequencyMap() and stored in PhenotypeLikelihoodRatio.hpoTerm2OverallFrequency).