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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 interface |
SignificantMotifOccurrencesFinder.JoinMethod
Interface for methods that combine several profiles over the same sequence into one common profile |
static class |
SignificantMotifOccurrencesFinder.RandomSeqType
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static class |
SignificantMotifOccurrencesFinder.SumOfProbabilities
Joins several profiles containing log-probabilities into one profile containing the logarithm of the sum of the probabilities of the single profiles. |
Constructor Summary | |
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SignificantMotifOccurrencesFinder(MotifDiscoverer disc,
DataSet bg,
double[] weights,
double sign)
This constructor creates an instance of SignificantMotifOccurrencesFinder that uses a DataSet to determine the siginificance level. |
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SignificantMotifOccurrencesFinder(MotifDiscoverer disc,
SignificantMotifOccurrencesFinder.JoinMethod joiner,
DataSet bg,
double[] weights,
double sign)
This constructor creates an instance of SignificantMotifOccurrencesFinder that uses a DataSet 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. |
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SignificantMotifOccurrencesFinder(MotifDiscoverer disc,
SignificantMotifOccurrencesFinder.RandomSeqType type,
SignificantMotifOccurrencesFinder.JoinMethod joiner,
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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DataSet |
annotateMotif(DataSet data,
int motifIndex)
This method annotates a DataSet . |
DataSet |
annotateMotif(DataSet data,
int motifIndex,
int addMax)
This method annotates a DataSet . |
DataSet |
annotateMotif(int startPos,
DataSet data,
int motifIndex)
This method annotates a DataSet starting in each sequence at startPos . |
DataSet |
annotateMotif(int startPos,
DataSet data,
int motifIndex,
int addMax,
boolean addAnnotation)
This method annotates a DataSet starting in each sequence at startPos . |
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. |
DataSet |
getBindingSites(DataSet data,
int motifIndex)
This method returns a DataSet containing the predicted binding sites. |
DataSet |
getBindingSites(int startPos,
DataSet data,
int motifIndex,
int addMax,
int addLeft,
int addRight)
This method returns a DataSet containing the predicted binding sites. |
double |
getFactorForAucPR()
This method returns a factor that must be multiplied to scores for computing PR curves. |
MotifDiscoverer |
getMotifDiscoverer()
This method returns a clone of the internally used MotifDiscoverer . |
double |
getNumberOfBoundSequences(DataSet data,
double[] weights,
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,
DataSet data,
int motifIndex,
int addMax)
This method returns a list of start positions of binding sites. |
double[][] |
getValuesForEachNucleotide(DataSet data,
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 . |
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, SignificantMotifOccurrencesFinder.RandomSeqType type, SignificantMotifOccurrencesFinder.JoinMethod joiner, 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 determinedjoiner
- the SignificantMotifOccurrencesFinder.JoinMethod
that defines how the profiles of the same motif in different components shall be joinedoneHistogram
- 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, DataSet bg, double[] weights, double sign)
SignificantMotifOccurrencesFinder
that uses a DataSet
to determine the siginificance level.
disc
- the MotifDiscoverer
for the predictionbg
- the background data setweights
- the weights of the background data set, can be null
sign
- the significance levelpublic SignificantMotifOccurrencesFinder(MotifDiscoverer disc, SignificantMotifOccurrencesFinder.JoinMethod joiner, DataSet bg, double[] weights, double sign)
SignificantMotifOccurrencesFinder
that uses a DataSet
to determine the siginificance level.
disc
- the MotifDiscoverer
for the predictionjoiner
- the SignificantMotifOccurrencesFinder.JoinMethod
that defines how the profiles of the same motif in different components shall be joinedbg
- the background data setweights
- the weights of the background data set, can be null
sign
- 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 DataSet annotateMotif(DataSet data, int motifIndex) throws Exception
DataSet
.
data
- the DataSet
motifIndex
- the index of the motif
DataSet
Exception
- if something went wrongannotateMotif(int, DataSet, int)
public DataSet annotateMotif(int startPos, DataSet data, int motifIndex) throws Exception
DataSet
starting in each sequence at startPos
.
startPos
- the start position used for all sequencesdata
- the DataSet
motifIndex
- the index of the motif
DataSet
Exception
- if something went wrongannotateMotif(int, DataSet, int)
public DataSet annotateMotif(DataSet data, int motifIndex, int addMax) throws Exception
DataSet
.
At most, addMax
motif occurrences of the motif instance will be annotated.
data
- the DataSet
motifIndex
- the index of the motifaddMax
- the number of motif occurrences that can at most be annotated for each motif instance
DataSet
Exception
- if something went wrongannotateMotif(int, DataSet, int)
public DataSet annotateMotif(int startPos, DataSet data, int motifIndex, int addMax, boolean addAnnotation) throws Exception
DataSet
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 DataSet
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
DataSet
Exception
- if something went wrongannotateMotif(int, DataSet, int)
public DataSet getBindingSites(DataSet data, int motifIndex) throws Exception
DataSet
containing the predicted binding sites.
data
- the DataSet
motifIndex
- the index of the motif
DataSet
containing the predicted binding sites
Exception
- if something went wrongpublic DataSet getBindingSites(int startPos, DataSet data, int motifIndex, int addMax, int addLeft, int addRight) throws Exception
DataSet
containing the predicted binding sites.
startPos
- the start position used for all sequencesdata
- the DataSet
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
DataSet
containing the predicted binding sites
Exception
- if something went wrongpublic IntList getStartPositions(int startPos, DataSet data, int motifIndex, int addMax) throws Exception
startPos
- the start position used for all sequencesdata
- the DataSet
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 double getNumberOfBoundSequences(DataSet data, double[] weights, int motifIndex) throws Exception
data
that are predicted to be bound at least once by motif no. motif
.
data
- the dataweights
- the weights of 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(DataSet, 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(DataSet, double[][], double, double, String)
public double getFactorForAucPR()
SignificantMotifOccurrencesFinder
was instantiated using oneHistogram=true
, the getValuesForEachNucleotide(DataSet, 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(DataSet, double[][], double, double, String)
public double[][] getValuesForEachNucleotide(DataSet data, int motif, boolean addOnlyBest) throws Exception
data
that this position is covered by at least one motif occurrence of the
motif with index index
. If the SignificantMotifOccurrencesFinder
was constructed using oneHistogram=true
the returned values are arbitrary scores, and p-values otherwise.
data
- the DataSet
motif
- 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(DataSet, double[][], double, double, String)
,
getOffsetForAucPR()
,
getFactorForAucPR()
public MotifDiscoverer getMotifDiscoverer() throws CloneNotSupportedException
MotifDiscoverer
.
MotifDiscoverer
CloneNotSupportedException
- if the MotifDiscoverer
can not be cloned correctly
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