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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,
boolean oneHistogram,
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 |
annotateMotif(int startPos,
Sample data,
int motifIndex)
This method annotates a Sample starting in each sequence at startPos . |
Sample |
annotateMotif(int startPos,
Sample data,
int motifIndex,
int addMax,
boolean addAnnotation)
This method annotates a Sample starting in each sequence at startPos . |
Sample |
annotateMotif(Sample data,
int motifIndex)
This method annotates a Sample . |
Sample |
annotateMotif(Sample data,
int motifIndex,
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. |
MotifAnnotation[] |
findSignificantMotifOccurrences(int motif,
Sequence seq,
int addMax,
int start)
This method finds the significant motif occurrences in the sequence. |
Sample |
getBindingSites(int startPos,
Sample data,
int motifIndex,
int addMax,
int addLeft,
int addRight)
This method returns a Sample containing the predicted binding sites. |
Sample |
getBindingSites(Sample data,
int motifIndex)
This method returns a Sample containing the predicted binding sites. |
double |
getFactorForAucPR()
This method returns a factor that must be multiplied to scores for computing PR curves. |
int |
getNumberOfBoundSequences(Sample data,
int motifIndex)
Returns the number of sequences in data that are predicted to be bound at least once by motif no. |
double |
getOffsetForAucPR()
This method returns an offset that must be added to scores for computing PR curves. |
IntList |
getStartPositions(int startPos,
Sample data,
int motifIndex,
int addMax)
This method returns a list of start positions of binding sites. |
double[][] |
getValuesForEachNucleotide(Sample data,
int component,
int motif,
boolean addOnlyBest)
This method determines a score for each possible starting position in each of the sequences in data
that this position is covered by at least 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, boolean oneHistogram, 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 determinedoneHistogram
- a switch to decide whether to use one background distribution histogram for all sequence or sequence specific background distribution histogramsnumSequences
- 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
- if the background sample could not be created, or some of the scores could not be computedpublic MotifAnnotation[] findSignificantMotifOccurrences(int motif, Sequence seq, int addMax, int start) throws Exception
motif
- the motif indexseq
- the sequenceaddMax
- the number of motif occurrences that can at most be annotatedstart
- the start position
MotifAnnotation
for the sequence
Exception
- if the background sample could not be created, or some of the scores could not be computedpublic Sample annotateMotif(Sample data, int motifIndex) throws Exception
Sample
.
data
- the Sample
motifIndex
- the index of the motif
Sample
Exception
- if something went wrongannotateMotif(int, Sample, int)
public Sample annotateMotif(int startPos, Sample data, int motifIndex) throws Exception
Sample
starting in each sequence at startPos
.
startPos
- the start position used for all sequencesdata
- the Sample
motifIndex
- the index of the motif
Sample
Exception
- if something went wrongannotateMotif(int, Sample, int)
public Sample annotateMotif(Sample data, int motifIndex, int addMax) throws Exception
Sample
.
At most, addMax
motif occurrences of the motif instance will be annotated.
data
- the Sample
motifIndex
- the index of the motifaddMax
- the number of motif occurrences that can at most be annotated for each motif instance
Sample
Exception
- if something went wrongannotateMotif(int, Sample, int)
public Sample annotateMotif(int startPos, Sample data, int motifIndex, int addMax, boolean addAnnotation) throws Exception
Sample
starting in each sequence at startPos
.
At most, addMax
motif occurrences of the motif instance will be annotated.
startPos
- the start position used for all sequencesdata
- the Sample
motifIndex
- the index of the motifaddMax
- the number of motif occurrences that can at most be annotated for each motif instanceaddAnnotation
- a switch whether to add or replace the current annotation
Sample
Exception
- if something went wrongannotateMotif(int, Sample, int)
public Sample getBindingSites(Sample data, int motifIndex) throws Exception
Sample
containing the predicted binding sites.
data
- the Sample
motifIndex
- the index of the motif
Sample
containing the predicted binding sites
Exception
- if something went wrongpublic Sample getBindingSites(int startPos, Sample data, int motifIndex, int addMax, int addLeft, int addRight) throws Exception
Sample
containing the predicted binding sites.
startPos
- the start position used for all sequencesdata
- the Sample
motifIndex
- the index of the motifaddMax
- the number of motif occurrences that can at most be annotated for each motif instanceaddLeft
- number of positions added to the left of the predicted motif occurrenceaddRight
- number of positions added to the right of the predicted motif occurrence
Sample
containing the predicted binding sites
Exception
- if something went wrongpublic IntList getStartPositions(int startPos, Sample data, int motifIndex, int addMax) throws Exception
startPos
- the start position used for all sequencesdata
- the Sample
motifIndex
- the index of the motifaddMax
- the number of motif occurrences that can at most be annotated for each motif instance
Exception
- if something went wrongpublic int getNumberOfBoundSequences(Sample data, int motifIndex) throws Exception
data
that are predicted to be bound at least once by motif no. motif
.
data
- the datamotifIndex
- the index of the motif
data
bound by motif motif
Exception
- if the background sample for the prediction could not be created or some of the scores could not be computedpublic double getOffsetForAucPR()
SignificantMotifOccurrencesFinder
was instantiated using oneHistogram=true
, the getValuesForEachNucleotide(Sample, int, int, boolean)
returns scores and no offset is needed. Otherwise,
it returns p-values and, hence, 1-(p-value) must be used for the PR curve and the offset is 1.
MotifDiscoveryAssessment.getSortedValuesForMotifAndFlanking(Sample, double[][], double, double, String)
public double getFactorForAucPR()
SignificantMotifOccurrencesFinder
was instantiated using oneHistogram=true
, the getValuesForEachNucleotide(Sample, int, int, boolean)
returns scores and a factor of 1 is appropriate. Otherwise,
it returns p-values and, hence, 1-(p-value) must be used for the PR curve and the factor is -1.
MotifDiscoveryAssessment.getSortedValuesForMotifAndFlanking(Sample, double[][], double, double, String)
public double[][] getValuesForEachNucleotide(Sample data, int component, int motif, boolean addOnlyBest) throws Exception
data
that this position is covered by at least one motif occurrence of the
motif with index index
in the component component
. If the SignificantMotifOccurrencesFinder
was constructed using oneHistogram=true
the returned values are arbitrary scores, and p-values otherwise.
data
- the Sample
component
- the component indexmotif
- the motif indexaddOnlyBest
- a switch whether to add only the best
Exception
- if something went wrong during the computation of the scores of the MotifDiscoverer
MotifDiscoveryAssessment.getSortedValuesForMotifAndFlanking(Sample, double[][], double, double, String)
,
getOffsetForAucPR()
,
getFactorForAucPR()
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