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java.lang.Objectde.jstacs.motifDiscovery.SignificantMotifOccurrencesFinder
public class SignificantMotifOccurrencesFinder
This class enables the user to predict motif occurrences given a specific significance level.
Nested Class Summary | |
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static class |
SignificantMotifOccurrencesFinder.RandomSeqType
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Constructor Summary | |
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SignificantMotifOccurrencesFinder(MotifDiscoverer disc,
Sample bg,
double sign)
This constructor creates an instance of SignificantMotifOccurrencesFinder that uses a Sample to determine the siginificance level. |
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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 | |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public SignificantMotifOccurrencesFinder(MotifDiscoverer disc, SignificantMotifOccurrencesFinder.RandomSeqType type, int numSequences, double sign)
SignificantMotifOccurrencesFinder
that uses the given SignificantMotifOccurrencesFinder.RandomSeqType
to determine the siginificance level.
disc
- the MotifDiscoverer
for the predictiontype
- the type that determines how the significance level is determinednumSequences
- the number of sampled sequence instances used to determine the significance levelsign
- the significance levelpublic SignificantMotifOccurrencesFinder(MotifDiscoverer disc, Sample bg, double sign)
SignificantMotifOccurrencesFinder
that uses a Sample
to determine the siginificance level.
disc
- the MotifDiscoverer
for the predictionbg
- the background data setsign
- the significance levelMethod Detail |
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public MotifAnnotation[] findSignificantMotifOccurrences(int motif, Sequence seq, int start) throws Exception
motif
- the motif indexseq
- the sequencestart
- the start position
MotifAnnotation
for the sequence
Exception
public Sample annotateMotifs(int startPos, Sample data) throws Exception
Sample
starting in each sequence at startPos
.
startPos
- the start position used for all sequencesdata
- the Sample
Sample
Exception
- if something went wrongannotateMotifs(int, Sample, int)
public Sample annotateMotifs(Sample data) throws Exception
Sample
.
data
- the Sample
Sample
Exception
- if something went wrongannotateMotifs(int, Sample, int)
public Sample annotateMotifs(Sample data, int addMax) throws Exception
Sample
.
At most, addMax
motif occurrences of each motif instance will be annotated.
data
- the Sample
addMax
- the number of motif occurrences that can at most be annotated for each motif instance
Sample
Exception
- if something went wrongannotateMotifs(int, Sample, int)
public Sample annotateMotifs(int startPos, Sample data, int addMax) throws Exception
Sample
starting in each sequence at startPos
.
At most, addMax
motif occurrences of each motif instance will be annotated.
startPos
- the start position used for all sequencesdata
- the Sample
addMax
- the number of motif occurrences that can at most be annotated for each motif instance
Sample
Exception
- if something went wrongannotateMotifs(int, Sample, int)
public double[][] getPValuesForEachNucleotide(Sample data, int component, int motif, boolean addOnlyBest) throws Exception
index
in the component component
.
data
- the Sample
component
- the component indexmotif
- the motif indexaddOnlyBest
- a switch whether to add only the best
p
-value for each symbol in the sequence
Exception
- if something went wrongMotifDiscoveryAssessment.getSorted1MinusPValuesForMotifAndFlanking(Sample, double[][], String)
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