public class KSGroupScorer extends GroupScorer
KS.computeOneSampleKS(int[], CDF)
. The data pumped into the KS is the positions relative to genes if the genes are of the
same length, or the straight hits from the motif finder otherwise.Scorer.ScoreSoftValueHashMap
Modifier and Type | Field and Description |
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(package private) static boolean |
debug |
groupMF, separateMotifFinders
lookupCount, mf, motifScoreCache2, usePrior
Constructor and Description |
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KSGroupScorer(MotifFinder genomicFinder,
MotifFinder groupFinder,
boolean discardOverlaps)
Sets the motif finder and discardOverlaps parameters of the motif finder appropriately and defaults the cdf for the uniform cdf with a
range [0..averageGeneLength] (if finder has uniform gene lengths) or [0..sequenceLength] (if finder has variable length genes).
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Modifier and Type | Method and Description |
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double |
calculateScore(Motif m)
Returns the score of m and increments the lookupCount.
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protected double |
calculateScore(MotifFinder groupMf,
FindResults groupFindResults,
MotifFinder organismMf,
FindResults organismFindResults,
double prior,
double motifLength)
Returns the -log likelihood that hits came from the CDF given in the constructor.
|
double |
calculateScore(MotifList ml)
Returns the -log probability that this motif is drawn from the CDF supplied in the constructor.
|
computePhi, computePhi, computePhi, getGenomicMotifFinder, getGroupCount, getGroupSize, getMotifFinder, setDiscardOverlaps, setMotifFinder, setSeparateMotifFinders
baseEntropy, computePrior, computePrior, getDiscardOverlaps, getLookupCount, getUsePrior, setScore, setScore, setScores, setScores, setUsePrior
public KSGroupScorer(MotifFinder genomicFinder, MotifFinder groupFinder, boolean discardOverlaps)
public double calculateScore(Motif m)
Scorer
calculateScore
in class Scorer
protected double calculateScore(MotifFinder groupMf, FindResults groupFindResults, MotifFinder organismMf, FindResults organismFindResults, double prior, double motifLength)
public double calculateScore(MotifList ml)
calculateScore
in class Scorer
CDF
,
KS.computeOneSampleKS(int[], CDF)
,
#calculateScore(int[], int[], double, double)