static MolecularSequence.Quality.Builder |
MolecularSequence.Quality.builder() |
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MolecularSequence.Quality.Builder |
MolecularSequence.Quality.Builder.end(Integer end) |
End position of the sequence.
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MolecularSequence.Quality.Builder |
MolecularSequence.Quality.Builder.end(java.lang.Integer end) |
Convenience method for setting end.
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MolecularSequence.Quality.Builder |
MolecularSequence.Quality.Builder.extension(Extension... extension) |
May be used to represent additional information that is not part of the basic definition of the element.
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MolecularSequence.Quality.Builder |
MolecularSequence.Quality.Builder.extension(java.util.Collection<Extension> extension) |
May be used to represent additional information that is not part of the basic definition of the element.
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protected MolecularSequence.Quality.Builder |
MolecularSequence.Quality.Builder.from(MolecularSequence.Quality quality) |
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MolecularSequence.Quality.Builder |
MolecularSequence.Quality.Builder.fScore(Decimal fScore) |
Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).
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MolecularSequence.Quality.Builder |
MolecularSequence.Quality.Builder.gtFP(Decimal gtFP) |
The number of false positives where the non-REF alleles in the Truth and Query Call Sets match (i.e.
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MolecularSequence.Quality.Builder |
MolecularSequence.Quality.Builder.id(java.lang.String id) |
Unique id for the element within a resource (for internal references).
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MolecularSequence.Quality.Builder |
MolecularSequence.Quality.Builder.method(CodeableConcept method) |
Which method is used to get sequence quality.
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MolecularSequence.Quality.Builder |
MolecularSequence.Quality.Builder.modifierExtension(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.
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MolecularSequence.Quality.Builder |
MolecularSequence.Quality.Builder.modifierExtension(java.util.Collection<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.
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MolecularSequence.Quality.Builder |
MolecularSequence.Quality.Builder.precision(Decimal precision) |
QUERY.TP / (QUERY.TP + QUERY.FP).
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MolecularSequence.Quality.Builder |
MolecularSequence.Quality.Builder.queryFP(Decimal queryFP) |
False positives, i.e.
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MolecularSequence.Quality.Builder |
MolecularSequence.Quality.Builder.queryTP(Decimal queryTP) |
True positives, from the perspective of the query data, i.e.
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MolecularSequence.Quality.Builder |
MolecularSequence.Quality.Builder.recall(Decimal recall) |
TRUTH.TP / (TRUTH.TP + TRUTH.FN).
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MolecularSequence.Quality.Builder |
MolecularSequence.Quality.Builder.roc(MolecularSequence.Quality.Roc roc) |
Receiver Operator Characteristic (ROC) Curve to give sensitivity/specificity tradeoff.
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MolecularSequence.Quality.Builder |
MolecularSequence.Quality.Builder.score(Quantity score) |
The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.
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MolecularSequence.Quality.Builder |
MolecularSequence.Quality.Builder.standardSequence(CodeableConcept standardSequence) |
Gold standard sequence used for comparing against.
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MolecularSequence.Quality.Builder |
MolecularSequence.Quality.Builder.start(Integer start) |
Start position of the sequence.
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MolecularSequence.Quality.Builder |
MolecularSequence.Quality.Builder.start(java.lang.Integer start) |
Convenience method for setting start.
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MolecularSequence.Quality.Builder |
MolecularSequence.Quality.toBuilder() |
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MolecularSequence.Quality.Builder |
MolecularSequence.Quality.Builder.truthFN(Decimal truthFN) |
False negatives, i.e.
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MolecularSequence.Quality.Builder |
MolecularSequence.Quality.Builder.truthTP(Decimal truthTP) |
True positives, from the perspective of the truth data, i.e.
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MolecularSequence.Quality.Builder |
MolecularSequence.Quality.Builder.type(QualityType type) |
INDEL / SNP / Undefined variant.
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