de.jstacs.motifDiscovery
Class SignificantMotifOccurrencesFinder

java.lang.Object
  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)