Data Model Libraries
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    MolecularSequenceQualityComponent Class

    FHIR Specification

    • Short: An set of value as quality of sequence
    • Definition: An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score (SO:0001686).

    Hierarchy (View Summary)

    Implements

    Index

    Constructors

    Properties

    Methods

    parse getTypeEnumType setTypeEnumType hasTypeEnumType getTypeElement setTypeElement hasTypeElement getType setType hasType getStandardSequence setStandardSequence hasStandardSequence getStartElement setStartElement hasStartElement getStart setStart hasStart getEndElement setEndElement hasEndElement getEnd setEnd hasEnd getScore setScore hasScore getMethod setMethod hasMethod getTruthTPElement setTruthTPElement hasTruthTPElement getTruthTP setTruthTP hasTruthTP getQueryTPElement setQueryTPElement hasQueryTPElement getQueryTP setQueryTP hasQueryTP getTruthFNElement setTruthFNElement hasTruthFNElement getTruthFN setTruthFN hasTruthFN getQueryFPElement setQueryFPElement hasQueryFPElement getQueryFP setQueryFP hasQueryFP getGtFPElement setGtFPElement hasGtFPElement getGtFP setGtFP hasGtFP getPrecisionElement setPrecisionElement hasPrecisionElement getPrecision setPrecision hasPrecision getRecallElement setRecallElement hasRecallElement getRecall setRecall hasRecall getFScoreElement setFScoreElement hasFScoreElement getFScore setFScore hasFScore getRoc setRoc hasRoc fhirType isEmpty isRequiredFieldsEmpty copy toJSON getModifierExtension setModifierExtension hasModifierExtension getModifierExtensionByUrl addModifierExtension removeModifierExtension getId setId hasId getExtension setExtension hasExtension getExtensionByUrl addExtension removeExtension isResource isDataType isComplexDataType isPrimitive isBooleanPrimitive isStringPrimitive isNumberPrimitive isBigIntPrimitive isDateTimePrimitive copyValues

    Constructors

    Properties

    qualityTypeEnum: QualityTypeEnum

    FHIR CodeSystem: QualityType

    type_: null | EnumCodeType

    MolecularSequence.quality.type Element

    FHIR Specification

    • Short: indel | snp | unknown
    • Definition: INDEL / SNP / Undefined variant.
    • FHIR Type: code
    • Cardinality: 1..1
    • isModifier: false
    • isSummary: true

    CodeSystem Enumeration: QualityTypeEnum

    standardSequence?: CodeableConcept

    MolecularSequence.quality.standardSequence Element

    FHIR Specification

    • Short: Standard sequence for comparison
    • Definition: Gold standard sequence used for comparing against.
    • FHIR Type: CodeableConcept
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true
    start?: IntegerType

    MolecularSequence.quality.start Element

    FHIR Specification

    • Short: Start position of the sequence
    • Definition: Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.
    • FHIR Type: integer
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true

    MolecularSequence.quality.end Element

    FHIR Specification

    • Short: End position of the sequence
    • Definition: 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.
    • FHIR Type: integer
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true
    score?: Quantity

    MolecularSequence.quality.score Element

    FHIR Specification

    • Short: Quality score for the comparison
    • Definition: The score of an experimentally derived feature such as a p-value (SO:0001685).
    • FHIR Type: Quantity
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true

    MolecularSequence.quality.method Element

    FHIR Specification

    • Short: Method to get quality
    • Definition: Which method is used to get sequence quality.
    • FHIR Type: CodeableConcept
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true
    truthTP?: DecimalType

    MolecularSequence.quality.truthTP Element

    FHIR Specification

    • Short: True positives from the perspective of the truth data
    • Definition: 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.
    • FHIR Type: decimal
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true
    queryTP?: DecimalType

    MolecularSequence.quality.queryTP Element

    FHIR Specification

    • Short: True positives from the perspective of the query data
    • Definition: 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.
    • FHIR Type: decimal
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true
    truthFN?: DecimalType

    MolecularSequence.quality.truthFN Element

    FHIR Specification

    • Short: False negatives
    • Definition: 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.
    • FHIR Type: decimal
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true
    queryFP?: DecimalType

    MolecularSequence.quality.queryFP Element

    FHIR Specification

    • Short: False positives
    • Definition: 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.
    • FHIR Type: decimal
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true

    MolecularSequence.quality.gtFP Element

    FHIR Specification

    • Short: False positives where the non-REF alleles in the Truth and Query Call Sets match
    • Definition: 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).
    • FHIR Type: decimal
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true
    precision?: DecimalType

    MolecularSequence.quality.precision Element

    FHIR Specification

    • Short: Precision of comparison
    • Definition: QUERY.TP / (QUERY.TP + QUERY.FP).
    • FHIR Type: decimal
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true
    recall?: DecimalType

    MolecularSequence.quality.recall Element

    FHIR Specification

    • Short: Recall of comparison
    • Definition: TRUTH.TP / (TRUTH.TP + TRUTH.FN).
    • FHIR Type: decimal
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true
    fScore?: DecimalType

    MolecularSequence.quality.fScore Element

    FHIR Specification

    • Short: F-score
    • Definition: Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).
    • FHIR Type: decimal
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true

    MolecularSequence.quality.roc Element

    FHIR Specification

    • Short: Receiver Operator Characteristic (ROC) Curve
    • Definition: Receiver Operator Characteristic (ROC) Curve to give sensitivity/specificity tradeoff.
    • FHIR Type: BackboneElement
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true

    Methods

    • Parse the provided MolecularSequenceQualityComponent JSON to instantiate the MolecularSequenceQualityComponent data model.

      Parameters

      • sourceJson: Value

        JSON representing FHIR MolecularSequenceQualityComponent

      • OptionaloptSourceField: string

        Optional data source field (e.g. <complexTypeName>.<complexTypeFieldName>); defaults to MolecularSequenceQualityComponent

      Returns undefined | MolecularSequenceQualityComponent

      MolecularSequenceQualityComponent data model or undefined for MolecularSequenceQualityComponent

      JsonError if the provided JSON is not a valid JSON object

    • Determines if the modifierExtension property exists.

      Parameters

      • Optionalurl: string

        the url that identifies a specific Extension

      Returns boolean

      true if an Extension has the provided url; false otherwise

      If the url is provided, determines if an Extension having the provided url exists. If the url is not provided, determines if the modifierExtension property exists and has any values.

      AssertionError for invalid url

    • Returns undefined | string

      the id property value

    • Assigns the provided value to the id property.

      Parameters

      • value: undefined | string

        the id value

      Returns this

      this

      PrimitiveTypeError for invalid value

    • Returns boolean

      true if id exists and has a value; false otherwise

    • Determines if the extension property exists.

      Parameters

      • Optionalurl: string

        the url that identifies a specific Extension

      Returns boolean

      true if an Extension has the provided url; false otherwise

      If the url is provided, determines if an Extension having the provided url exists. If the url is not provided, determines if the extension property exists and has any values.

      AssertionError for invalid url

    • Determines if the extension property exists.

      Parameters

      • url: string

        the url that identifies a specific Extension

      Returns undefined | IExtension

      an Extension having the provided url

      If the url is provided, determines if an Extension having the provided url exists. If the url is not provided, determines if the extension property exists and has any values.

      AssertionError for invalid url

    • Adds the provided Extension to the extension property array.

      Parameters

      • extension: undefined | IExtension

        the Extension value to add to the extension property array

      Returns this

      this

    • Removes the Extension having the provided url from the extension property array.

      Parameters

      • url: string

        the url that identifies a specific Extension to remove

      Returns void

      AssertionError for invalid url

    • Returns boolean

      true if the instance is a FHIR complex or primitive datatype; false otherwise