public class RatioScorer extends OccurrenceScorer
A LAPLACE correction of 1 is added to guard against zero counts.
Scorer.ScoreSoftValueHashMap
Modifier and Type | Field and Description |
---|---|
protected MarkovModel |
denominatorMM |
static int |
LAPLACE
The a pseuodo count that is added to all counts in the ratio calculations.
|
protected MarkovModel |
numeratorMM |
WOC
groupMF, separateMotifFinders
lookupCount, mf, motifScoreCache2, usePrior
Constructor and Description |
---|
RatioScorer(MotifFinder denominatorFinder,
MotifFinder numeratorFinder,
boolean discardOverlaps)
Sets the motif finder to be hte denominatorFinder and the group motif finder to be the numeratorFinder and tells them whether or not to
discard overlaps.
|
Modifier and Type | Method and Description |
---|---|
protected double |
calculateScore(int groupCount,
int totalCount,
double prior,
int length)
This is only used if calculateScore(MotifList) is caled -- computes the score based on the groupCount and total count as the log_2
ratio of groupCount / totalCount.
|
double |
calculateScore(Motif m)
Returns the score of m.
|
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 LAPLACE
protected MarkovModel numeratorMM
protected MarkovModel denominatorMM
public RatioScorer(MotifFinder denominatorFinder, MotifFinder numeratorFinder, boolean discardOverlaps)
protected double calculateScore(int groupCount, int totalCount, double prior, int length)
LAPLACE
.calculateScore
in class OccurrenceScorer
public double calculateScore(Motif m)
OccurrenceScorer
calculateScore
in class OccurrenceScorer