Uses of Class
org.monarchinitiative.lirical.core.analysis.AnalysisOptions.Builder

Packages that use AnalysisOptions.Builder

Package	Description
org.monarchinitiative.lirical.core.analysis	A high-level representation of LIRICAL analysis.

Uses of AnalysisOptions.Builder in org.monarchinitiative.lirical.core.analysis

Methods in org.monarchinitiative.lirical.core.analysis that return AnalysisOptions.Builder

Modifier and Type	Method	Description
AnalysisOptions.Builder	AnalysisOptions.Builder.addDiseaseDatabases(Collection<org.monarchinitiative.phenol.annotations.io.hpo.DiseaseDatabase> diseaseDatabases)
AnalysisOptions.Builder	AnalysisOptions.Builder.addDiseaseDatabases(org.monarchinitiative.phenol.annotations.io.hpo.DiseaseDatabase... diseaseDatabases)
AnalysisOptions.Builder	AnalysisOptions.Builder.addTargetDiseases(Collection<org.monarchinitiative.phenol.ontology.data.TermId> diseaseIds)
AnalysisOptions.Builder	AnalysisOptions.Builder.addTargetDiseases(org.monarchinitiative.phenol.ontology.data.TermId... diseaseIds)
static AnalysisOptions.Builder	AnalysisOptions.builder()
AnalysisOptions.Builder	AnalysisOptions.Builder.clearDiseaseDatabases()
AnalysisOptions.Builder	AnalysisOptions.Builder.clearTargetDiseases()
AnalysisOptions.Builder	AnalysisOptions.Builder.defaultVariantBackgroundFrequency(double defaultVariantBackgroundFrequency)
AnalysisOptions.Builder	AnalysisOptions.Builder.genomeBuild(GenomeBuild genomeBuild)
AnalysisOptions.Builder	AnalysisOptions.Builder.includeDiseasesWithNoDeleteriousVariants(boolean includeDiseasesWithNoDeleteriousVariants)
AnalysisOptions.Builder	AnalysisOptions.Builder.pretestProbability(PretestDiseaseProbability pretestDiseaseProbability)
AnalysisOptions.Builder	AnalysisOptions.Builder.setDiseaseDatabases(Collection<org.monarchinitiative.phenol.annotations.io.hpo.DiseaseDatabase> diseaseDatabases)
AnalysisOptions.Builder	AnalysisOptions.Builder.setTargetDiseases(Collection<org.monarchinitiative.phenol.ontology.data.TermId> diseaseIds)
AnalysisOptions.Builder	AnalysisOptions.Builder.transcriptDatabase(TranscriptDatabase transcriptDatabase)
AnalysisOptions.Builder	AnalysisOptions.Builder.useGlobal(boolean useGlobal)
AnalysisOptions.Builder	AnalysisOptions.Builder.useStrictPenalties(boolean useStrictPenalties)
AnalysisOptions.Builder	AnalysisOptions.Builder.variantDeleteriousnessThreshold(float variantDeleteriousnessThreshold)