public class RelativeEntropyScorer extends GroupScorer
PWM
Scorer.ScoreSoftValueHashMap
Modifier and Type | Field and Description |
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protected int |
HD
The hamming space around which to expand each motif.
|
static int |
WOC
The wildcard optimization cutoff used for the motif finders.
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groupMF, separateMotifFinders
lookupCount, mf, motifScoreCache2, usePrior
Constructor and Description |
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RelativeEntropyScorer(MotifFinder referenceFinder,
MotifFinder testFinder,
boolean discardOverlaps,
int hammingDistance)
Sets the motif finder and discardOverlaps parameters of the motif finder appropriately; hammingDistance determines the space into which
we will expand each motif.
|
Modifier and Type | Method and Description |
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double |
calculateScore(Motif m)
The conservation of this motif as measured by the relative entropy of the PWM of this motif and it's neighbors in the test motif finder
versus in the reference motif finder.
|
double |
calculateScore(MotifList ml)
This method has not been implemented.
|
computePhi, computePhi, computePhi, getGenomicMotifFinder, getGroupCount, getGroupSize, getMotifFinder, setDiscardOverlaps, setMotifFinder, setSeparateMotifFinders
baseEntropy, computePrior, computePrior, getDiscardOverlaps, getLookupCount, getUsePrior, setScore, setScore, setScores, setScores, setUsePrior
public static final int WOC
protected int HD
public RelativeEntropyScorer(MotifFinder referenceFinder, MotifFinder testFinder, boolean discardOverlaps, int hammingDistance)
public double calculateScore(Motif m)
calculateScore
in class Scorer
PWM.computeRelativeEntropy(PWM)
public double calculateScore(MotifList ml)
calculateScore
in class Scorer
java.lang.IllegalArgumentException
- since this method has not been implemented.