Package org.monarchinitiative.lirical.core.analysis

Interface AnalysisOptions

public interface AnalysisOptions
A container for analysis-specific settings, i.e. settings that need to be changed for analysis of each sample.

  • Method Details

    • builder

      static AnalysisOptions.Builder builder()

    • genomeBuild

      GenomeBuild genomeBuild()
      Returns:
      genome build to use in the analysis or null to run a phenotype-only analysis.

    • transcriptDatabase

      TranscriptDatabase transcriptDatabase()
      Returns:
      the transcript database that should be used in this analysis.

    • diseaseDatabases

      Set<org.monarchinitiative.phenol.annotations.io.hpo.DiseaseDatabase> diseaseDatabases()
      Returns:
      evaluate the patient wrt. diseases from given source(s).

    • targetDiseases

      Collection<org.monarchinitiative.phenol.ontology.data.TermId> targetDiseases()
      Limit the analysis to specific diseases.
      Returns:
      a collection of disease IDs of the diseases of interest or null if all diseases should be tested.

    • variantDeleteriousnessThreshold

      float variantDeleteriousnessThreshold()
      Returns:
      threshold for determining if the variant is deleterious or not. The threshold range must be in range of [0,1].

    • defaultVariantBackgroundFrequency

      double defaultVariantBackgroundFrequency()
      Returns:
      default frequency of called-pathogenic variants in the general population o use if for whatever reason, data was not available in gnomAD.

    • useStrictPenalties

      boolean useStrictPenalties()
      Returns:
      true if strict penalties should be used if the genotype does not match the disease model in terms of number of called pathogenic alleles.

    • useGlobal

      boolean useGlobal()
      Returns:
      true if the global analysis mode should be used.

    • pretestDiseaseProbability

      PretestDiseaseProbability pretestDiseaseProbability()
      Returns:
      pretest disease probability container.

    • includeDiseasesWithNoDeleteriousVariants

      boolean includeDiseasesWithNoDeleteriousVariants()
      Include a disease if no known or predicted deleterious variants are found in the gene associated with the disease. The option is used only if the variants are available for the investigated individual.
      Returns:
      true if the candidate disease should be disregarded.