Package edu.cornell.med.icb.tissueinfo.similarity.scorers

Interface Summary

ExpressionProfileSimilarityScorer

Implementations of this interface can be used to score the similarity of two expression profiles.

Class Summary

BaselineNormalizedConfidenceScorer	Confidence scorer normalized with BaselineNormalizedScorer.
BaselineNormalizerScorer	A scorer that normalizes the score produced by another scorer given the sums of EST counts in the query and target.
BinaryConfidenceScorer
BinaryScorer
EstRepresentationScorer	Same as RawESTScorer, but divides raw counts by the number of EST in the particular tissue plus one.
ExpressionConfidenceScorer	Implements the scorer described in http://icb.med.cornell.edu/wiki/uploads/math/c/2/8/c280e1c6b3550fcff8e2dc01676f923a.png.
FastExpressionConfidenceScorer	Optimized version of ExpressionConfidenceScorer with fixed confidence thresholds.
KendallTauScorer	Scores two transcript by calculating the Kendall's tau measure between their tissue expression profiles.
MaxNormalizedConfidenceScorer	Confidence scorer normalized with MaxNormalizedScorer.
MaxNormalizerScorer	A scorer that normalizes the score produced by another scorer given the maximum score that could be obtained against each of the scored transcripts.
NormalizedBinaryScorer	Binary scorer normalized with NormalizedScorer.
NormalizedConfidenceScorer	Confidence scorer normalized with NormalizedScorer.
NormalizerScorer	A scorer that normalizes the score produced by another scorer given the number of EST counts that are not zero in the query and target.
PearsonScorer	Scores two transcript by calculating the Pearson correlation coefficient between their tissue expression profiles.
RawEstCountScorer	Implements the scheme described in http://icb.med.cornell.edu/wiki/uploads/math/c/2/8/c280e1c6b3550fcff8e2dc01676f923a.png, but without transforming raw counts into confidence values.
ShuffleNormalizedBinaryScorer	Created by IntelliJ IDEA.
ShuffleNormalizedConfidenceScorer
ShuffleNormalizerScorer	A scorer that normalizes the score produced by another scorer given the average scored observed when shuffling the counts.