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HS.FHIRModel.R4.MolecularSequenceX.Quality

class HS.FHIRModel.R4.MolecularSequenceX.Quality extends HS.FHIRModel.FHIRClassSuper

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** MolecularSequenceX.Quality generated class schema
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Raw data describing a biological sequence.

Property Inventory

Method Inventory

Parameters

parameter XMLTYPE = R4_MOLECULARSEQUENCEX_QUALITY;
Inherited description: This parameter provides the default XMLTYPE for the class. If it is empty then the class name will be used to construct a default XML type.

The default XMLTYPE is used when naming and referencing this type in a schema and the schema context did not provide an XML type name.

Properties

property _end as HS.FHIRModel.R4.Element;
Extensions for end
Property methods: _endGet(), _endGetSwizzled(), _endIsValid(), _endNewObject(), _endSet()
property _fScore as HS.FHIRModel.R4.Element;
Extensions for fScore
Property methods: _fScoreGet(), _fScoreGetSwizzled(), _fScoreIsValid(), _fScoreNewObject(), _fScoreSet()
property _gtFP as HS.FHIRModel.R4.Element;
Extensions for gtFP
Property methods: _gtFPGet(), _gtFPGetSwizzled(), _gtFPIsValid(), _gtFPNewObject(), _gtFPSet()
property _precision as HS.FHIRModel.R4.Element;
Extensions for precision
Property methods: _precisionGet(), _precisionGetSwizzled(), _precisionIsValid(), _precisionNewObject(), _precisionSet()
property _queryFP as HS.FHIRModel.R4.Element;
Extensions for queryFP
Property methods: _queryFPGet(), _queryFPGetSwizzled(), _queryFPIsValid(), _queryFPNewObject(), _queryFPSet()
property _queryTP as HS.FHIRModel.R4.Element;
Extensions for queryTP
Property methods: _queryTPGet(), _queryTPGetSwizzled(), _queryTPIsValid(), _queryTPNewObject(), _queryTPSet()
property _recall as HS.FHIRModel.R4.Element;
Extensions for recall
Property methods: _recallGet(), _recallGetSwizzled(), _recallIsValid(), _recallNewObject(), _recallSet()
property _start as HS.FHIRModel.R4.Element;
Extensions for start
Property methods: _startGet(), _startGetSwizzled(), _startIsValid(), _startNewObject(), _startSet()
property _truthFN as HS.FHIRModel.R4.Element;
Extensions for truthFN
Property methods: _truthFNGet(), _truthFNGetSwizzled(), _truthFNIsValid(), _truthFNNewObject(), _truthFNSet()
property _truthTP as HS.FHIRModel.R4.Element;
Extensions for truthTP
Property methods: _truthTPGet(), _truthTPGetSwizzled(), _truthTPIsValid(), _truthTPNewObject(), _truthTPSet()
property _type as HS.FHIRModel.R4.Element;
Extensions for type
Property methods: _typeGet(), _typeGetSwizzled(), _typeIsValid(), _typeNewObject(), _typeSet()
property end as %Integer;
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.
Property methods: endDisplayToLogical(), endGet(), endIsValid(), endLogicalToDisplay(), endNormalize(), endSet(), endXSDToLogical()
property extension as HS.FHIRModel.R4.SeqOfExtension;
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.
Property methods: extensionGet(), extensionGetSwizzled(), extensionIsValid(), extensionNewObject(), extensionSet()
property fScore as %Integer;
Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).
Property methods: fScoreDisplayToLogical(), fScoreGet(), fScoreIsValid(), fScoreLogicalToDisplay(), fScoreNormalize(), fScoreSet(), fScoreXSDToLogical()
property fhirID as %String;
Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
Property methods: fhirIDDisplayToLogical(), fhirIDGet(), fhirIDIsValid(), fhirIDLogicalToDisplay(), fhirIDLogicalToOdbc(), fhirIDNormalize(), fhirIDSet()
property gtFP as %Integer;
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).
Property methods: gtFPDisplayToLogical(), gtFPGet(), gtFPIsValid(), gtFPLogicalToDisplay(), gtFPNormalize(), gtFPSet(), gtFPXSDToLogical()
property method as HS.FHIRModel.R4.CodeableConcept;
Which method is used to get sequence quality.
Property methods: methodGet(), methodGetSwizzled(), methodIsValid(), methodNewObject(), methodSet()
property modifierExtension as HS.FHIRModel.R4.SeqOfExtension;
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).
Property methods: modifierExtensionGet(), modifierExtensionGetSwizzled(), modifierExtensionIsValid(), modifierExtensionNewObject(), modifierExtensionSet()
property precision as %Integer;
QUERY.TP / (QUERY.TP + QUERY.FP).
Property methods: precisionDisplayToLogical(), precisionGet(), precisionIsValid(), precisionLogicalToDisplay(), precisionNormalize(), precisionSet(), precisionXSDToLogical()
property queryFP as %Integer;
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.
Property methods: queryFPDisplayToLogical(), queryFPGet(), queryFPIsValid(), queryFPLogicalToDisplay(), queryFPNormalize(), queryFPSet(), queryFPXSDToLogical()
property queryTP as %Integer;
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.
Property methods: queryTPDisplayToLogical(), queryTPGet(), queryTPIsValid(), queryTPLogicalToDisplay(), queryTPNormalize(), queryTPSet(), queryTPXSDToLogical()
property recall as %Integer;
TRUTH.TP / (TRUTH.TP + TRUTH.FN).
Property methods: recallDisplayToLogical(), recallGet(), recallIsValid(), recallLogicalToDisplay(), recallNormalize(), recallSet(), recallXSDToLogical()
Receiver Operator Characteristic (ROC) Curve to give sensitivity/specificity tradeoff.
Property methods: rocGet(), rocGetSwizzled(), rocIsValid(), rocNewObject(), rocSet()
property score as HS.FHIRModel.R4.Quantity;
The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685)).
Property methods: scoreGet(), scoreGetSwizzled(), scoreIsValid(), scoreNewObject(), scoreSet()
property standardSequence as HS.FHIRModel.R4.CodeableConcept;
Gold standard sequence used for comparing against.
Property methods: standardSequenceGet(), standardSequenceGetSwizzled(), standardSequenceIsValid(), standardSequenceNewObject(), standardSequenceSet()
property start as %Integer;
Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.
Property methods: startDisplayToLogical(), startGet(), startIsValid(), startLogicalToDisplay(), startNormalize(), startSet(), startXSDToLogical()
property truthFN as %Integer;
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.
Property methods: truthFNDisplayToLogical(), truthFNGet(), truthFNIsValid(), truthFNLogicalToDisplay(), truthFNNormalize(), truthFNSet(), truthFNXSDToLogical()
property truthTP as %Integer;
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.
Property methods: truthTPDisplayToLogical(), truthTPGet(), truthTPIsValid(), truthTPLogicalToDisplay(), truthTPNormalize(), truthTPSet(), truthTPXSDToLogical()
property type as %String (VALUELIST = ",indel,snp,unknown");
INDEL / SNP / Undefined variant.
Property methods: typeDisplayToLogical(), typeGet(), typeIsValid(), typeLogicalToDisplay(), typeLogicalToOdbc(), typeNormalize(), typeSet()

Methods

method IncludeExtension()
method IncludeMethod()
method IncludeModifierExtension()
method IncludeRoc()
method IncludeScore()
method IncludeStandardSequence()
method _getProperties() as %DynamicArray
Inherited description: Return an array of the defined properties of this class in the definition order that they were discovered in the the HL7FHIR JSchema document
method toDao() as %DynamicAbstractObject
Inherited description: >

The toDao() method casts the set to a DAO.

Inherited Members

Inherited Methods

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