public class GeneSetResamplingPvalGenerator extends AbstractGeneSetPvalGenerator
Modifier and Type | Field and Description |
---|---|
protected GeneSetResamplingBackgroundDistributionGenerator |
generator |
protected Histogram |
hist |
ALERT_UPDATE_FREQUENCY, geneAnnots, geneToScoreMap, messenger, numGenesUsed, settings
Constructor and Description |
---|
GeneSetResamplingPvalGenerator(GeneSetResamplingPvalGenerator toclone,
Map<Gene,Double> geneToScoreMap)
Clone a generator; don't recompute the background.
|
GeneSetResamplingPvalGenerator(SettingsHolder settings,
GeneAnnotations a,
Map<Gene,Double> geneToScoreMap,
StatusViewer messenger) |
Modifier and Type | Method and Description |
---|---|
GeneSetResult |
classPval(GeneSetTerm geneSetName)
Get results for one class, based on class id.
|
Map<GeneSetTerm,Double> |
classPvalGeneratorRaw()
Same thing as classPval, but returns a more raw map of genesets to scores (pvalues) (see below) instead of adding
them to the results object.
|
Map<GeneSetTerm,GeneSetResult> |
generateGeneSetResults()
Compute the results for all the gene sets under consideration.
|
protected Map<GeneSetTerm,GeneSetResult> |
generateGeneSetResults(boolean useMultifunctionalityCorrection) |
protected double |
scoreToPval(int geneSetSize,
double rawscore)
Convert a raw score into a pvalue, based on background distribution
|
checkAspect, checkAspectAndRedundancy, getMaxClassSize, getMessenger, getMinGeneSetSize, getNumGenesUsed, multipleTestCorrect, numGenesInSet, numProbesInSet, ranksOfGenesInSet, set_class_max_size, set_class_min_size
ifInterruptedStop
protected Histogram hist
protected GeneSetResamplingBackgroundDistributionGenerator generator
public GeneSetResamplingPvalGenerator(SettingsHolder settings, GeneAnnotations a, Map<Gene,Double> geneToScoreMap, StatusViewer messenger)
settings
- a
- geneToScoreMap
- already log-transformed, if requested.messenger
- public GeneSetResamplingPvalGenerator(GeneSetResamplingPvalGenerator toclone, Map<Gene,Double> geneToScoreMap)
toclone
- geneToScoreMap
- public Map<GeneSetTerm,GeneSetResult> generateGeneSetResults()
AbstractGeneSetPvalGenerator
generateGeneSetResults
in class AbstractGeneSetPvalGenerator
protected Map<GeneSetTerm,GeneSetResult> generateGeneSetResults(boolean useMultifunctionalityCorrection)
useMultifunctionalityCorrection
- public GeneSetResult classPval(GeneSetTerm geneSetName)
geneSetName
- groupToPvalMap
- probesToPvals
- public Map<GeneSetTerm,Double> classPvalGeneratorRaw()
protected double scoreToPval(int geneSetSize, double rawscore)
geneSetSize
- the size of the gene set that this score is for (used to identify which distribution to use)rawscore
- the raw score of the gene setCopyright © 2002-2013 UBC Centre for High-Throughput Biology. All Rights Reserved.