Package org.monarchinitiative.lirical.core.analysis

Interface AnalysisData

public interface AnalysisData
Representation of subject data required by LIRICAL analysis.

  • Method Details

    • of

      static AnalysisData of(String sampleId, Age age, Sex sex, Collection<org.monarchinitiative.phenol.ontology.data.TermId> presentPhenotypeTerms, Collection<org.monarchinitiative.phenol.ontology.data.TermId> negatedPhenotypeTerms, GenesAndGenotypes genes)
      Construct analysis data from the inputs.
      Parameters:
      sampleId - non-null sample identifier.
      age - subject's age or null if not available.
      sex - non-null sex.
      presentPhenotypeTerms - a collection of observed HPO terms.
      negatedPhenotypeTerms - a collection of excluded HPO terms.
      genes - non-null container of genes and genotypes.

    • sampleId

      String sampleId()
      Returns:
      a non-null sample ID.

    • age

      Optional<Age> age()
      Returns:
      an optional with age or empty optional if age is not available.

    • sex

      Sex sex()
      Returns:
      a non-null sex of the subject.

    • presentPhenotypeTerms

      List<org.monarchinitiative.phenol.ontology.data.TermId> presentPhenotypeTerms()
      Returns:
      a list of the HPO terms that were observed in the subject.

    • negatedPhenotypeTerms

      List<org.monarchinitiative.phenol.ontology.data.TermId> negatedPhenotypeTerms()
      Returns:
      a list of the HPO terms whose presence was explicitly excluded in the subject.

    • genes

      GenesAndGenotypes genes()
      Returns:
      container with genes and genotypes observed in the subject.