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java.lang.Object de.jstacs.motifDiscovery.MotifDiscoveryAssessment
public class MotifDiscoveryAssessment
This class enables the user to assess the prediction of motif occurrences
Constructor Summary | |
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MotifDiscoveryAssessment()
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Method Summary | |
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static ListResult |
assess(Sample truth,
Sample prediction,
int maxDiff)
This method computes the nucleotide and site measures. |
static double[][] |
getSortedScoresForMotifAndFlanking(Sample data,
Sample pred,
String identifier)
Returns the scores read from the prediction pred for the motif with identifier identifier and flanking sequences as annotated in
the Sample data. |
static double[][] |
getSortedValuesForMotifAndFlanking(Sample data,
double[][] values,
double offset,
double factor,
String identifier)
This method provides some score arrays that can be used in ScoreBasedPerformanceMeasureDefinitions to determine some
curves or area under curves based on the values of the predictions. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public MotifDiscoveryAssessment()
Method Detail |
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public static ListResult assess(Sample truth, Sample prediction, int maxDiff) throws Exception
truth
- the Sample
annotated with the true annotationprediction
- annotated with the predicted annotationmaxDiff
- the maximal difference between predicted and true start position;
this value is used to determine the site measures
ListResult
containing all NumericalResultSet
s
Exception
- if something went wrongpublic static double[][] getSortedValuesForMotifAndFlanking(Sample data, double[][] values, double offset, double factor, String identifier)
ScoreBasedPerformanceMeasureDefinitions
to determine some
curves or area under curves based on the values of the predictions. The scores are generated by offset+factor*values[i][j]
.
data
- the datavalues
- the array of smoothed valuesoffset
- the offset that is added to the current valuesfactor
- the factor that is multiplied to the current valuesidentifier
- the identifier of the annotation of the positive class
SequenceAnnotation.getIdentifier()
public static double[][] getSortedScoresForMotifAndFlanking(Sample data, Sample pred, String identifier)
pred
for the motif with identifier identifier
and flanking sequences as annotated in
the Sample
data. The identifier
may be null
to obtain the scores for all motifs, irrespective of present identifiers.
The first dimension of the returned array contains the scores for the motif annotations, while the second dimension contains the scores of the flanking sequences.
Both dimensions are sorted and can be directly used in the methods of ScoreBasedPerformanceMeasureDefinitions
.
The scores for the predictions must be added to the LocatedSequenceAnnotationWithLength
representing the motifs as additional annotation using LocatedSequenceAnnotationWithLength.LocatedSequenceAnnotationWithLength(String, String, LocatedSequenceAnnotation[], Result...)
with the name of the annotation, i.e. the name of the corresponding Result
equal to "score".
data
- the Sample
annotated with the truthpred
- the Sample
annotated with the prediction and associated scoresidentifier
- the identifier of the motif
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