MolecularSequenceQuality constructor
- @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;