public class LogOccurrenceScorer extends OccurrenceScorer
Poisson
distribution class. Thus, the genomic finder sets
the background probability that any given motif will be this particular motif. Note that no LAPLACE corrections are given, so motifs that
occur in the group motif finder and not in the genomic finder will yield scores of INFINITY. It thus is only statistically valid if the
group motif finder represents a subset of genomic motif finder, as that guarentees that no occurrences in the group will be absent in the
genome.Scorer.ScoreSoftValueHashMap
Modifier and Type | Field and Description |
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static int |
WOC
The wildcard optimization cutoff used for the motif finders.
|
groupMF, separateMotifFinders
lookupCount, mf, motifScoreCache2, usePrior
Constructor and Description |
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LogOccurrenceScorer(MotifFinder genomicFinder,
MotifFinder groupFinder,
boolean discardOverlaps)
Sets the motif finder and group motif finder and tells them whether or not to discard overlaps.
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Modifier and Type | Method and Description |
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protected double |
calculateScore(double groupCount,
double totalCount,
double prior,
int length)
Computes the score based on the groupCount, total count, a prior to use, and a motif length for calculating the probability that any
given motif is this motif.
|
double |
calculateScore(Motif m)
Returns the score of m.
|
double |
calculateScore(MotifList ml)
Calculates the score of ml using the sum of the group counts and total counts of all motifs in ml and using the average prior and motif
length.
|
protected double |
logCount(MotifFinder finder,
Motif m)
Returns sum_i [ln(f_im + 1)] where f_im is the number of occurrences of motif m in gene i.
|
protected double |
logCount(MotifFinder finder,
MotifList ml)
Returns sum_i [ln(f_im + 1)] where f_im is the number of occurrences of MotifList m in gene i.
|
protected double |
transform(double d) |
calculateScore
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
public LogOccurrenceScorer(MotifFinder genomicFinder, MotifFinder groupFinder, boolean discardOverlaps)
protected double calculateScore(double groupCount, double totalCount, double prior, int length)
public double calculateScore(Motif m)
calculateScore
in class OccurrenceScorer
public double calculateScore(MotifList ml)
calculateScore
in class OccurrenceScorer
protected double logCount(MotifFinder finder, Motif m)
protected double logCount(MotifFinder finder, MotifList ml)
protected double transform(double d)