de.jstacs.motifDiscovery
Class SignificantMotifOccurrencesFinder

java.lang.Object
  extended by de.jstacs.motifDiscovery.SignificantMotifOccurrencesFinder

public class SignificantMotifOccurrencesFinder
extends Object

This class enables the user to predict motif occurrences given a specific significance level.

Author:
Jan Grau, Jens Keilwagen

Nested Class Summary
static class SignificantMotifOccurrencesFinder.RandomSeqType
           
 
Constructor Summary
SignificantMotifOccurrencesFinder(MotifDiscoverer disc, Sample bg, double sign)
          This constructor creates an instance of SignificantMotifOccurrencesFinder that uses a Sample to determine the siginificance level.
SignificantMotifOccurrencesFinder(MotifDiscoverer disc, SignificantMotifOccurrencesFinder.RandomSeqType type, int numSequences, double sign)
          This constructor creates an instance of SignificantMotifOccurrencesFinder that uses the given SignificantMotifOccurrencesFinder.RandomSeqType to determine the siginificance level.
 
Method Summary
 Sample annotateMotifs(int startPos, Sample data)
          This method annotates a Sample starting in each sequence at startPos.
 Sample annotateMotifs(int startPos, Sample data, int addMax)
          This method annotates a Sample starting in each sequence at startPos.
 Sample annotateMotifs(Sample data)
          This method annotates a Sample.
 Sample annotateMotifs(Sample data, int addMax)
          This method annotates a Sample.
 MotifAnnotation[] findSignificantMotifOccurrences(int motif, Sequence seq, int start)
          This method finds the significant motif occurrences in the sequence.
 double[][] getPValuesForEachNucleotide(Sample data, int component, int motif, boolean addOnlyBest)
          This method determines the p-value for each symbol to be annotated at least in one motif occurrence of the motif with index index in the component component.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SignificantMotifOccurrencesFinder

public SignificantMotifOccurrencesFinder(MotifDiscoverer disc,
                                         SignificantMotifOccurrencesFinder.RandomSeqType type,
                                         int numSequences,
                                         double sign)
This constructor creates an instance of SignificantMotifOccurrencesFinder that uses the given SignificantMotifOccurrencesFinder.RandomSeqType to determine the siginificance level.

Parameters:
disc - the MotifDiscoverer for the prediction
type - the type that determines how the significance level is determined
numSequences - the number of sampled sequence instances used to determine the significance level
sign - the significance level

SignificantMotifOccurrencesFinder

public SignificantMotifOccurrencesFinder(MotifDiscoverer disc,
                                         Sample bg,
                                         double sign)
This constructor creates an instance of SignificantMotifOccurrencesFinder that uses a Sample to determine the siginificance level.

Parameters:
disc - the MotifDiscoverer for the prediction
bg - the background data set
sign - the significance level
Method Detail

findSignificantMotifOccurrences

public MotifAnnotation[] findSignificantMotifOccurrences(int motif,
                                                         Sequence seq,
                                                         int start)
                                                  throws Exception
This method finds the significant motif occurrences in the sequence.

Parameters:
motif - the motif index
seq - the sequence
start - the start position
Returns:
an array of MotifAnnotation for the sequence
Throws:
Exception

annotateMotifs

public Sample annotateMotifs(int startPos,
                             Sample data)
                      throws Exception
This method annotates a Sample starting in each sequence at startPos.

Parameters:
startPos - the start position used for all sequences
data - the Sample
Returns:
an annotated Sample
Throws:
Exception - if something went wrong
See Also:
annotateMotifs(int, Sample, int)

annotateMotifs

public Sample annotateMotifs(Sample data)
                      throws Exception
This method annotates a Sample.

Parameters:
data - the Sample
Returns:
an annotated Sample
Throws:
Exception - if something went wrong
See Also:
annotateMotifs(int, Sample, int)

annotateMotifs

public Sample annotateMotifs(Sample data,
                             int addMax)
                      throws Exception
This method annotates a Sample. At most, addMax motif occurrences of each motif instance will be annotated.

Parameters:
data - the Sample
addMax - the number of motif occurrences that can at most be annotated for each motif instance
Returns:
an annotated Sample
Throws:
Exception - if something went wrong
See Also:
annotateMotifs(int, Sample, int)

annotateMotifs

public Sample annotateMotifs(int startPos,
                             Sample data,
                             int addMax)
                      throws Exception
This method annotates a Sample starting in each sequence at startPos. At most, addMax motif occurrences of each motif instance will be annotated.

Parameters:
startPos - the start position used for all sequences
data - the Sample
addMax - the number of motif occurrences that can at most be annotated for each motif instance
Returns:
an annotated Sample
Throws:
Exception - if something went wrong
See Also:
annotateMotifs(int, Sample, int)

getPValuesForEachNucleotide

public double[][] getPValuesForEachNucleotide(Sample data,
                                              int component,
                                              int motif,
                                              boolean addOnlyBest)
                                       throws Exception
This method determines the p-value for each symbol to be annotated at least in one motif occurrence of the motif with index index in the component component.

Parameters:
data - the Sample
component - the component index
motif - the motif index
addOnlyBest - a switch whether to add only the best
Returns:
an array containing for each sequence an array with the p-value for each symbol in the sequence
Throws:
Exception - if something went wrong
See Also:
MotifDiscoveryAssessment.getSorted1MinusPValuesForMotifAndFlanking(Sample, double[][], String)