Package org.hl7.fhir.r4.model

Class MolecularSequence.MolecularSequenceQualityComponent

java.lang.Object
org.hl7.fhir.r4.model.Base
org.hl7.fhir.r4.model.Element
org.hl7.fhir.r4.model.BackboneElement
org.hl7.fhir.r4.model.MolecularSequence.MolecularSequenceQualityComponent
All Implemented Interfaces:
ca.uhn.fhir.model.api.IElement, Serializable, org.hl7.fhir.instance.model.api.IBase, org.hl7.fhir.instance.model.api.IBaseBackboneElement, org.hl7.fhir.instance.model.api.IBaseElement, org.hl7.fhir.instance.model.api.IBaseHasExtensions, org.hl7.fhir.instance.model.api.IBaseHasModifierExtensions
Enclosing class:
MolecularSequence
public static class MolecularSequence.MolecularSequenceQualityComponent extends BackboneElement implements org.hl7.fhir.instance.model.api.IBaseBackboneElement
See Also:

  • Field Details

    • type

      protected Enumeration<MolecularSequence.QualityType> type
      INDEL / SNP / Undefined variant.

    • standardSequence

      protected CodeableConcept standardSequence
      Gold standard sequence used for comparing against.

    • start

      protected IntegerType start
      Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.

    • end

      protected IntegerType end
      End position of the sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.

    • score

      protected Quantity score
      The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685)).

    • method

      protected CodeableConcept method
      Which method is used to get sequence quality.

    • truthTP

      protected DecimalType truthTP
      True positives, from the perspective of the truth data, i.e. the number of sites in the Truth Call Set for which there are paths through the Query Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.

    • queryTP

      protected DecimalType queryTP
      True positives, from the perspective of the query data, i.e. the number of sites in the Query Call Set for which there are paths through the Truth Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.

    • truthFN

      protected DecimalType truthFN
      False negatives, i.e. the number of sites in the Truth Call Set for which there is no path through the Query Call Set that is consistent with all of the alleles at this site, or sites for which there is an inaccurate genotype call for the event. Sites with correct variant but incorrect genotype are counted here.

    • queryFP

      protected DecimalType queryFP
      False positives, i.e. the number of sites in the Query Call Set for which there is no path through the Truth Call Set that is consistent with this site. Sites with correct variant but incorrect genotype are counted here.

    • gtFP

      protected DecimalType gtFP
      The number of false positives where the non-REF alleles in the Truth and Query Call Sets match (i.e. cases where the truth is 1/1 and the query is 0/1 or similar).

    • precision

      protected DecimalType precision
      QUERY.TP / (QUERY.TP + QUERY.FP).

    • recall

      protected DecimalType recall
      TRUTH.TP / (TRUTH.TP + TRUTH.FN).

    • fScore

      protected DecimalType fScore
      Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).

    • roc

      protected MolecularSequence.MolecularSequenceQualityRocComponent roc
      Receiver Operator Characteristic (ROC) Curve to give sensitivity/specificity tradeoff.

  • Constructor Details

  • Method Details