Package | Description |
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ubic.erminej.analysis | |
ubic.erminej.data | |
ubic.erminej.gui.geneset.edit |
Modifier and Type | Field and Description |
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protected Map<Gene,Double> |
AbstractGeneSetPvalGenerator.geneToScoreMap |
Modifier and Type | Method and Description |
---|---|
Collection<Gene> |
OraPvalGenerator.getGenesAboveThreshold() |
Modifier and Type | Method and Description |
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protected double |
GeneSetResamplingBackgroundDistributionGenerator.averagePrecision(Collection<Gene> genesInSet) |
protected GeneSetResult |
OraPvalGenerator.classPval(Collection<Gene> genesAboveThresh,
GeneSetTerm className)
Get results for one class, based on class id.
|
double |
GeneSetResamplingBackgroundDistributionGenerator.computeRawScore(double[] genevalues,
Collection<Gene> genesInSet)
Basic method to calculate the raw score for a gene set, given an array of the gene scores for items in the class.
|
protected List<Double> |
AbstractGeneSetPvalGenerator.ranksOfGenesInSet(Collection<Gene> genesInSet) |
Constructor and Description |
---|
AbstractGeneSetPvalGenerator(SettingsHolder set,
GeneAnnotations annots,
Map<Gene,Double> geneToScoreMap,
StatusViewer messenger) |
ExperimentScoreQuickPvalGenerator(SettingsHolder settings,
GeneAnnotations a,
Map<Gene,Double> geneToScoreMap,
StatusViewer messenger) |
GeneSetResamplingBackgroundDistributionGenerator(SettingsHolder settings,
Map<Gene,Double> geneToScoreMap) |
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) |
RocPvalGenerator(SettingsHolder set,
GeneAnnotations an,
Map<Gene,Double> geneToScoreMap,
StatusViewer messenger) |
Modifier and Type | Method and Description |
---|---|
Gene |
GeneAnnotations.findGene(String symbol)
Case insensitive
|
Gene |
Probe.getGene() |
Gene |
Multifunctionality.getMostMultifunctional(Collection<Gene> genes)
Convenience method.
|
Modifier and Type | Method and Description |
---|---|
Map<Gene,Double> |
Multifunctionality.adjustScores(Map<Gene,Double> geneToScoreMap,
boolean useRanks,
boolean weight)
Given a set of scores for genes, adjust them to correct for multifunctionality, using a regression approach.
|
Collection<Gene> |
GeneAnnotations.getGenes()
Return all genes, including those that are 'inactive'.
|
Collection<Gene> |
Probe.getGenes() |
Set<Gene> |
GeneSet.getGenes()
Do not modify this collection directly! Use 'addGene'.
|
Set<Gene> |
GeneAnnotations.getGeneSetGenes(GeneSetTerm goset) |
Map<Gene,Double> |
GeneScores.getGeneToScoreMap()
Note that these values will already be log tranformed if that was requested.
|
Map<Gene,Double> |
GeneScores.getGeneToScoreMap(boolean shuffle) |
List<Gene> |
GeneScores.getRankedGenes() |
Collection<Gene> |
UserDefinedGeneSetManager.loadPlainGeneList(String fileName)
Read in a list of genes or probe ids from a file.
|
Collection<Gene> |
GeneAnnotations.loadPlainGeneList(String loadFile) |
Map<Gene,Double> |
Multifunctionality.padogWeights() |
Modifier and Type | Method and Description |
---|---|
int |
GeneAnnotations.addAnnotation(Gene gene,
Collection<GeneSetTerm> terms) |
protected void |
Probe.addGene(Gene g) |
void |
GeneSet.addGene(Gene g)
Add the gene (and its probes)
|
int |
Gene.compareTo(Gene o) |
double |
Multifunctionality.getMultifunctionalityRank(Gene gene) |
double |
Multifunctionality.getMultifunctionalityScore(Gene gene) |
int |
Multifunctionality.getNumGoTerms(Gene gene) |
Double |
Multifunctionality.getRawGeneMultifunctionalityRank(Gene gene) |
boolean |
GeneAnnotations.hasGene(Gene g) |
int |
GeneAnnotations.numProbesForGene(Gene g)
Get how many probes point to the same gene.
|
void |
Probe.setGene(Gene g)
Assumes we only have one gene per probe.
|
Modifier and Type | Method and Description |
---|---|
void |
GeneSet.addGenes(Collection<Gene> gs) |
void |
GeneAnnotations.addGeneSet(GeneSetTerm geneSetId,
Collection<Gene> gs) |
GeneSet |
GeneAnnotations.addGeneSet(GeneSetTerm geneSetId,
Collection<Gene> gs,
String sourceFile)
Add a user-defined gene set.
|
Map<Gene,Double> |
Multifunctionality.adjustScores(Map<Gene,Double> geneToScoreMap,
boolean useRanks,
boolean weight)
Given a set of scores for genes, adjust them to correct for multifunctionality, using a regression approach.
|
double |
Multifunctionality.correlationWithGeneMultifunctionality(List<Gene> rankedGenes) |
double |
Multifunctionality.enrichmentForMultifunctionality(Collection<Gene> genesInSet)
This is like correlationWithGeneMultifunctionality(List
|
double |
Multifunctionality.enrichmentForMultifunctionalityPvalue(Collection<Gene> genesInSet) |
Gene |
Multifunctionality.getMostMultifunctional(Collection<Gene> genes)
Convenience method.
|
GeneAnnotations |
GeneAnnotationParser.readDefault(InputStream bis,
Collection<Gene> activeGenes,
SettingsHolder settings,
boolean simple)
Main default reading method.
|
GeneAnnotations |
GeneAnnotationParser.readDefault(String fileName,
Collection<Gene> genes,
SettingsHolder settings,
boolean simple) |
void |
Probe.setGenes(Collection<Gene> genes) |
void |
GeneSet.setGenes(Collection<Gene> genes) |
Constructor and Description |
---|
GeneAnnotations(Collection<Gene> genes,
GeneSetTerms geneSetTerms,
SettingsHolder settings,
StatusViewer messenger) |
GeneAnnotations(List<Gene> geneSymbols,
List<Collection<GeneSetTerm>> goTerms,
StatusViewer m)
Constructor designed for use when a file is not the immediate input of the data.
|
GeneSet(GeneSetTerm name,
Collection<Gene> items) |
Probe(String name,
String description,
Collection<Gene> genes) |
Modifier and Type | Method and Description |
---|---|
protected void |
GeneSetWizardStep2.setStartingSet(Collection<Gene> genes) |
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