de.jstacs.motifDiscovery
Class MotifDiscoveryAssessment
java.lang.Object
de.jstacs.motifDiscovery.MotifDiscoveryAssessment
public class MotifDiscoveryAssessment
- extends Object
This class enables the user to assess the prediction of motif occurrences
- Author:
- Jan Grau, Jens Keilwagen
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
MotifDiscoveryAssessment
public MotifDiscoveryAssessment()
assess
public static ListResult assess(Sample truth,
Sample prediction,
int maxDiff)
throws Exception
- This method computes the nucleotide and site measures.
- Parameters:
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
- Returns:
- a
ListResult
containing all NumericalResultSet
s
- Throws:
Exception
- if something went wrong
getSorted1MinusPValuesForMotifAndFlanking
public static double[][] getSorted1MinusPValuesForMotifAndFlanking(Sample data,
double[][] pValues,
String identifier)
throws Exception
- This method provides some score arrays that can be used in
ScoreBasedPerformanceMeasureDefinitions
to determine some
curves or area under curves based on the p
-values of the predictions.
- Parameters:
data
- the datapValues
- the p-valueidentifier
- the identifier of the annotation of the positive class
- Returns:
- two arrays containing 1-
p
-value; the first contains the values for the positive class, the second contains
the values for the negative class
- Throws:
Exception
- See Also:
SequenceAnnotation.getIdentifier()