MolecularSequenceQuality constructor

const MolecularSequenceQuality({ @JsonKey(name: 'id') FhirId? fhirId, @JsonKey(name: 'extension') List<FhirExtension>? extension_, List<FhirExtension>? modifierExtension, FhirCode? type, @JsonKey(name: '_type') Element? typeElement, CodeableConcept? standardSequence, FhirInteger? start, @JsonKey(name: '_start') Element? startElement, FhirInteger? end, @JsonKey(name: '_end') Element? endElement, Quantity? score, CodeableConcept? method, FhirDecimal? truthTP, @JsonKey(name: '_truthTP') Element? truthTPElement, FhirDecimal? queryTP, @JsonKey(name: '_queryTP') Element? queryTPElement, FhirDecimal? truthFN, @JsonKey(name: '_truthFN') Element? truthFNElement, FhirDecimal? queryFP, @JsonKey(name: '_queryFP') Element? queryFPElement, FhirDecimal? gtFP, @JsonKey(name: '_gtFP') Element? gtFPElement, FhirDecimal? precision, @JsonKey(name: '_precision') Element? precisionElement, FhirDecimal? recall, @JsonKey(name: '_recall') Element? recallElement, FhirDecimal? fScore, @JsonKey(name: '_fScore') Element? fScoreElement, MolecularSequenceRoc? roc, })

MolecularSequenceQuality Raw data describing a biological sequence.

id Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

extension_ May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

modifierExtension May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

type INDEL / SNP / Undefined variant.

typeElement Extensions for type

standardSequence Gold standard sequence used for comparing against.

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

startElement Extensions for start

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.

endElement Extensions for end

score The score of an experimentally derived feature such as a p-value (SO:0001685).

method Which method is used to get sequence quality.

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.

truthTPElement Extensions for truthTP

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.

queryTPElement Extensions for queryTP

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.

truthFNElement Extensions for truthFN

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.

queryFPElement Extensions for queryFP

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).

gtFPElement Extensions for gtFP

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

precisionElement Extensions for precision

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

recallElement Extensions for recall

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

fScoreElement Extensions for fScore

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

Implementation

const factory MolecularSequenceQuality({
  /// [id] Unique id for the element within a resource (for internal
  ///  references). This may be any string value that does not contain spaces.
  @JsonKey(name: 'id') FhirId? fhirId,

  /// [extension_] May be used to represent additional information that is not
  /// part of the basic definition of the element. To make the use of extensions
  /// safe and manageable, there is a strict set of governance  applied to the
  /// definition and use of extensions. Though any implementer can define an
  /// extension, there is a set of requirements that SHALL be met as part of the
  ///  definition of the extension.
  @JsonKey(name: 'extension') List<FhirExtension>? extension_,

  /// [modifierExtension] May be used to represent additional information that
  /// is not part of the basic definition of the element and that modifies the
  /// understanding of the element in which it is contained and/or the
  /// understanding of the containing element's descendants. Usually modifier
  /// elements provide negation or qualification. To make the use of extensions
  /// safe and manageable, there is a strict set of governance applied to the
  /// definition and use of extensions. Though any implementer can define an
  /// extension, there is a set of requirements that SHALL be met as part of the
  /// definition of the extension. Applications processing a resource are
  ///  required to check for modifier extensions.
  /// Modifier extensions SHALL NOT change the meaning of any elements on
  /// Resource or DomainResource (including cannot change the meaning of
  ///  modifierExtension itself).
  List<FhirExtension>? modifierExtension,

  /// [type] INDEL / SNP / Undefined variant.
  FhirCode? type,

  /// [typeElement] Extensions for type
  @JsonKey(name: '_type') Element? typeElement,

  /// [standardSequence] Gold standard sequence used for comparing against.
  CodeableConcept? standardSequence,

  /// [start] Start position of the sequence. If the coordinate system is
  ///  either 0-based or 1-based, then start position is inclusive.
  FhirInteger? start,

  /// [startElement] Extensions for start
  @JsonKey(name: '_start') Element? startElement,

  /// [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.
  FhirInteger? end,

  /// [endElement] Extensions for end
  @JsonKey(name: '_end') Element? endElement,

  /// [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)).
  Quantity? score,

  /// [method] Which method is used to get sequence quality.
  CodeableConcept? method,

  /// [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.
  FhirDecimal? truthTP,

  /// [truthTPElement] Extensions for truthTP
  @JsonKey(name: '_truthTP') Element? truthTPElement,

  /// [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.
  FhirDecimal? queryTP,

  /// [queryTPElement] Extensions for queryTP
  @JsonKey(name: '_queryTP') Element? queryTPElement,

  /// [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.
  FhirDecimal? truthFN,

  /// [truthFNElement] Extensions for truthFN
  @JsonKey(name: '_truthFN') Element? truthFNElement,

  /// [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.
  FhirDecimal? queryFP,

  /// [queryFPElement] Extensions for queryFP
  @JsonKey(name: '_queryFP') Element? queryFPElement,

  /// [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).
  FhirDecimal? gtFP,

  /// [gtFPElement] Extensions for gtFP
  @JsonKey(name: '_gtFP') Element? gtFPElement,

  /// [precision] QUERY.TP / (QUERY.TP + QUERY.FP).
  FhirDecimal? precision,

  /// [precisionElement] Extensions for precision
  @JsonKey(name: '_precision') Element? precisionElement,

  /// [recall] TRUTH.TP / (TRUTH.TP + TRUTH.FN).
  FhirDecimal? recall,

  /// [recallElement] Extensions for recall
  @JsonKey(name: '_recall') Element? recallElement,

  /// [fScore] Harmonic mean of Recall and Precision, computed as: 2 *
  ///  precision * recall / (precision + recall).
  FhirDecimal? fScore,

  /// [fScoreElement] Extensions for fScore
  @JsonKey(name: '_fScore') Element? fScoreElement,

  /// [roc] Receiver Operator Characteristic (ROC) Curve  to give
  ///  sensitivity/specificity tradeoff.
  MolecularSequenceRoc? roc,
}) = _MolecularSequenceQuality;