de.jstacs.motifDiscovery
Class MotifDiscoveryAssessment

java.lang.Object
  extended by 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

Constructor Summary
MotifDiscoveryAssessment()
           
 
Method Summary
static ListResult assess(Sample truth, Sample prediction, int maxDiff)
          This method computes the nucleotide and site measures.
static double[][] getSorted1MinusPValuesForMotifAndFlanking(Sample data, double[][] pValues, 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 p-values of the predictions.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

MotifDiscoveryAssessment

public MotifDiscoveryAssessment()
Method Detail

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 annotation
prediction - annotated with the predicted annotation
maxDiff - the maximal difference between predicted and true start position; this value is used to determine the site measures
Returns:
a ListResult containing all NumericalResultSets
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 data
pValues - the p-value
identifier - 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()