public class ZScoreScorer extends Scorer
The motif finder that this scorer holds on to is the motif finder returned by the wrapped scorer's getMotifFinder() method, or getGenomicMotifFinder() method if it's a group scorer.
There is no such thing as a prior for this scorer. It's setting will be ignored.
Note that this is a slow scorer and is intended for use in normalizing the scores of several Scorers.
Scorer.ScoreSoftValueHashMap
Modifier and Type | Field and Description |
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protected int |
numTrials |
protected Scorer |
scorer |
lookupCount, mf, motifScoreCache2, usePrior
Constructor and Description |
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ZScoreScorer(Scorer scorer,
int numTrials)
Sets the scorer that this will use to the given scorer.
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Modifier and Type | Method and Description |
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double |
calculateScore(Motif m)
Calculates the Z-score of this motif by sampling numTrials (as specified in constructor) motifs from the regions where m is found.
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double |
calculateScore(MotifList ml)
This has not been implemented.
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protected Motif[] |
getScrambled(Motif m) |
baseEntropy, computePhi, computePhi, computePhi, computePrior, computePrior, getDiscardOverlaps, getLookupCount, getMotifFinder, getUsePrior, setDiscardOverlaps, setMotifFinder, setScore, setScore, setScores, setScores, setUsePrior
protected int numTrials
protected Scorer scorer
public ZScoreScorer(Scorer scorer, int numTrials)
public double calculateScore(Motif m)
SearchUtils.getRandomNeighbors(int, Motif, MotifFinder
so it's compared to all the motifs around it.calculateScore
in class Scorer
public double calculateScore(MotifList ml)
calculateScore
in class Scorer
java.lang.IllegalArgumentException
- Because this method has not been implemented.