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Class TMolecularSequenceQuality

Description
Hierarchy
Fields
Methods
Properties

Unit

bsFhir_r4b

Declaration

type TMolecularSequenceQuality = class(TBackboneElement)

Description

Raw data describing a biological sequence.

Hierarchy

Overview

Methods

Public constructor Create; override;

Properties

Public property type_ : string read Gettype_ write Settype_;
Public property type_Element : TqualityType read Gettype_Element write Settype_Element;
Public property standardSequence : TCodeableConcept read GetstandardSequence write SetstandardSequence;
Public property start : integer read Getstart write Setstart;
Public property startElement : Tinteger read GetstartElement write SetstartElement;
Public property end_ : integer read Getend_ write Setend_;
Public property end_Element : Tinteger read Getend_Element write Setend_Element;
Public property score : TQuantity read Getscore write Setscore;
Public property method : TCodeableConcept read Getmethod write Setmethod;
Public property truthTP : Double read GettruthTP write SettruthTP;
Public property truthTPElement : Tdecimal read GettruthTPElement write SettruthTPElement;
Public property queryTP : Double read GetqueryTP write SetqueryTP;
Public property queryTPElement : Tdecimal read GetqueryTPElement write SetqueryTPElement;
Public property truthFN : Double read GettruthFN write SettruthFN;
Public property truthFNElement : Tdecimal read GettruthFNElement write SettruthFNElement;
Public property queryFP : Double read GetqueryFP write SetqueryFP;
Public property queryFPElement : Tdecimal read GetqueryFPElement write SetqueryFPElement;
Public property gtFP : Double read GetgtFP write SetgtFP;
Public property gtFPElement : Tdecimal read GetgtFPElement write SetgtFPElement;
Public property precision : Double read Getprecision write Setprecision;
Public property precisionElement : Tdecimal read GetprecisionElement write SetprecisionElement;
Public property recall : Double read Getrecall write Setrecall;
Public property recallElement : Tdecimal read GetrecallElement write SetrecallElement;
Public property fScore : Double read GetfScore write SetfScore;
Public property fScoreElement : Tdecimal read GetfScoreElement write SetfScoreElement;
Public property roc : TMolecularSequenceRoc read Getroc write Setroc;

Description

Methods

Public constructor Create; override;
 

Properties

Public property type_ : string read Gettype_ write Settype_;

INDEL / SNP / Undefined variant.

Public property type_Element : TqualityType read Gettype_Element write Settype_Element;
 
Public property standardSequence : TCodeableConcept read GetstandardSequence write SetstandardSequence;

Gold standard sequence used for comparing against.

Public property start : integer read Getstart write Setstart;

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

Public property startElement : Tinteger read GetstartElement write SetstartElement;
 
Public property end_ : integer read Getend_ write Setend_;

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.

Public property end_Element : Tinteger read Getend_Element write Setend_Element;
 
Public property score : TQuantity read Getscore write Setscore;

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

Public property method : TCodeableConcept read Getmethod write Setmethod;

Which method is used to get sequence quality.

Public property truthTP : Double read GettruthTP write SettruthTP;

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.

Public property truthTPElement : Tdecimal read GettruthTPElement write SettruthTPElement;
 
Public property queryTP : Double read GetqueryTP write SetqueryTP;

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.

Public property queryTPElement : Tdecimal read GetqueryTPElement write SetqueryTPElement;
 
Public property truthFN : Double read GettruthFN write SettruthFN;

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.

Public property truthFNElement : Tdecimal read GettruthFNElement write SettruthFNElement;
 
Public property queryFP : Double read GetqueryFP write SetqueryFP;

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.

Public property queryFPElement : Tdecimal read GetqueryFPElement write SetqueryFPElement;
 
Public property gtFP : Double read GetgtFP write SetgtFP;

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).

Public property gtFPElement : Tdecimal read GetgtFPElement write SetgtFPElement;
 
Public property precision : Double read Getprecision write Setprecision;

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

Public property precisionElement : Tdecimal read GetprecisionElement write SetprecisionElement;
 
Public property recall : Double read Getrecall write Setrecall;

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

Public property recallElement : Tdecimal read GetrecallElement write SetrecallElement;
 
Public property fScore : Double read GetfScore write SetfScore;

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

Public property fScoreElement : Tdecimal read GetfScoreElement write SetfScoreElement;
 
Public property roc : TMolecularSequenceRoc read Getroc write Setroc;

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

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