Modifier and Type | Method and Description |
---|---|
void |
Settings.setSelectedCustomGeneSets(Collection<GeneSetTerm> addedClasses) |
Modifier and Type | Method and Description |
---|---|
Map<GeneSetTerm,Double> |
GeneSetResamplingPvalGenerator.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> |
RocPvalGenerator.generateGeneSetResults() |
Map<GeneSetTerm,GeneSetResult> |
CorrelationPvalGenerator.generateGeneSetResults() |
Map<GeneSetTerm,GeneSetResult> |
OraPvalGenerator.generateGeneSetResults() |
abstract Map<GeneSetTerm,GeneSetResult> |
AbstractGeneSetPvalGenerator.generateGeneSetResults()
Compute the results for all the gene sets under consideration.
|
Map<GeneSetTerm,GeneSetResult> |
GeneSetResamplingPvalGenerator.generateGeneSetResults() |
protected Map<GeneSetTerm,GeneSetResult> |
RocPvalGenerator.generateGeneSetResults(boolean useMultifunctionalityCorrection) |
protected Map<GeneSetTerm,GeneSetResult> |
GeneSetResamplingPvalGenerator.generateGeneSetResults(boolean useMultifunctionalityCorrection) |
Map<GeneSetTerm,GeneSetResult> |
GeneSetPvalRun.getResults() |
static List<GeneSetTerm> |
GeneSetPvalRun.getSortedClasses(Map<GeneSetTerm,GeneSetResult> results) |
static List<GeneSetTerm> |
GeneSetPvalRun.getSortedClasses(Map<GeneSetTerm,GeneSetResult> results,
boolean useMfCorrection) |
static List<GeneSetTerm> |
GeneSetPvalRun.populateRanks(Map<GeneSetTerm,GeneSetResult> results)
Fill in the ranks
|
Modifier and Type | Method and Description |
---|---|
protected boolean |
AbstractGeneSetPvalGenerator.checkAspect(GeneSetTerm geneSetName,
boolean missingAspectTreatedAsUsable) |
protected boolean |
AbstractGeneSetPvalGenerator.checkAspectAndRedundancy(GeneSetTerm geneSetName)
If GO data isn't initialized, this returns true.
|
protected GeneSetResult |
OraPvalGenerator.classPval(Collection<Gene> genesAboveThresh,
GeneSetTerm className)
Get results for one class, based on class id.
|
GeneSetResult |
CorrelationPvalGenerator.classPval(GeneSetTerm geneSetName) |
GeneSetResult |
GeneSetResamplingPvalGenerator.classPval(GeneSetTerm geneSetName)
Get results for one class, based on class id.
|
double |
ExperimentScoreQuickPvalGenerator.classPvalue(GeneSetTerm geneSetName)
This is stripped-down version of classPvalue.
|
int |
AbstractGeneSetPvalGenerator.numGenesInSet(GeneSetTerm t) |
int |
AbstractGeneSetPvalGenerator.numProbesInSet(GeneSetTerm t) |
Modifier and Type | Method and Description |
---|---|
static List<GeneSetTerm> |
GeneSetPvalRun.getSortedClasses(Map<GeneSetTerm,GeneSetResult> results) |
static List<GeneSetTerm> |
GeneSetPvalRun.getSortedClasses(Map<GeneSetTerm,GeneSetResult> results,
boolean useMfCorrection) |
protected void |
AbstractGeneSetPvalGenerator.multipleTestCorrect(List<GeneSetTerm> sortedClasses,
Map<GeneSetTerm,GeneSetResult> results)
Perform multiple test correction during the multifunctionality correction.
|
protected void |
AbstractGeneSetPvalGenerator.multipleTestCorrect(List<GeneSetTerm> sortedClasses,
Map<GeneSetTerm,GeneSetResult> results)
Perform multiple test correction during the multifunctionality correction.
|
static List<GeneSetTerm> |
GeneSetPvalRun.populateRanks(Map<GeneSetTerm,GeneSetResult> results)
Fill in the ranks
|
Constructor and Description |
---|
GeneSetPvalRun(SettingsHolder settings,
GeneAnnotations originalAnnots,
StatusViewer messenger,
Map<GeneSetTerm,GeneSetResult> results,
String name)
Use this when we are loading in existing results from a file.
|
MultipleTestCorrector(SettingsHolder set,
List<GeneSetTerm> sc,
GeneAnnotations geneData,
GeneScores geneScores,
Map<GeneSetTerm,GeneSetResult> results,
StatusViewer messenger) |
MultipleTestCorrector(SettingsHolder set,
List<GeneSetTerm> sc,
GeneAnnotations geneData,
GeneScores geneScores,
Map<GeneSetTerm,GeneSetResult> results,
StatusViewer messenger) |
Modifier and Type | Field and Description |
---|---|
protected GeneSetTerm |
GeneSetResult.geneSetTerm |
Modifier and Type | Method and Description |
---|---|
GeneSetTerm |
GeneAnnotations.findTerm(String id) |
protected GeneSetTerm |
GeneSetTerms.get(String geneSetId)
Note that it is probably preferable to use findTerm from GeneAnnotations; this is used while setting that up.
|
GeneSetTerm |
GeneSetDetails.getClassID() |
GeneSetTerm |
GeneSetResult.getGeneSetId() |
GeneSetTerm |
GeneSet.getTerm() |
Modifier and Type | Method and Description |
---|---|
Set<GeneSetTerm> |
GeneAnnotations.findSetsByGene(String searchOn)
Identify gene sets that contain a particular gene or probe.
|
Set<GeneSetTerm> |
GeneAnnotations.findSetsByName(String searchOn) |
Set<GeneSetTerm> |
GeneSetTerms.getAllChildren(GeneSetTerm term) |
Collection<GeneSetTerm> |
GeneSetTerms.getAllParents(GeneSetTerm id) |
Set<GeneSetTerm> |
GeneAnnotations.getAllTerms()
Get all gene sets, including ones that might be empty or redundant.
|
Set<GeneSetTerm> |
GeneAnnotations.getChildren(GeneSetTerm id) |
Set<GeneSetTerm> |
GeneSetTerms.getChildren(GeneSetTerm id) |
DirectedGraph<String,GeneSetTerm> |
GeneAnnotations.getGeneSetGraph() |
Set<GeneSetTerm> |
GeneSetTerms.getGeneSets() |
Collection<GeneSetTerm> |
Probe.getGeneSets() |
Collection<GeneSetTerm> |
Gene.getGeneSets() |
Set<GeneSetTerm> |
GeneAnnotations.getGeneSetTerms() |
Map<String,GeneSetTerm> |
GOParser.getGONameMap()
Get a simple Map that contains keys that are the GO ids, values are the names.
|
DirectedGraph<String,GeneSetTerm> |
GeneSetTerms.getGraph() |
DirectedGraph<String,GeneSetTerm> |
GOParser.getGraph()
Get the graph that was created.
|
Collection<GeneSetTerm> |
GeneSetTerms.getParents(GeneSetTerm id) |
Collection<GeneSetTerm> |
GeneSetTerms.getTerms() |
Set<GeneSetTerm> |
GeneAnnotations.getUserDefinedTerms()
Get the gene sets that are user-defined.
|
Collection<GeneSetTerm> |
GeneAnnotations.selectUserDefined()
Make the selection the user-defined sets only.
|
Modifier and Type | Method and Description |
---|---|
boolean |
Gene.addGeneSet(GeneSetTerm t)
Updates membership (for probes too).
|
void |
GeneAnnotations.addGeneSet(GeneSetTerm geneSetId,
Collection<Gene> gs) |
GeneSet |
GeneAnnotations.addGeneSet(GeneSetTerm geneSetId,
Collection<Gene> gs,
String sourceFile)
Add a user-defined gene set.
|
void |
Probe.addToGeneSet(GeneSetTerm geneSet) |
int |
GeneSetTerm.compareTo(GeneSetTerm o) |
void |
GeneAnnotations.deleteGeneSet(GeneSetTerm id)
Remove a gene set (class) from all the maps that reference it.
|
boolean |
UserDefinedGeneSetManager.deleteUserGeneSet(GeneSetTerm termToDelete)
Delete a user-defined gene set from disk and from the annotations in memory.
|
boolean |
GeneAnnotations.deleteUserGeneSet(GeneSetTerm classID) |
GeneSet |
GeneAnnotations.findGeneSet(GeneSetTerm term) |
Set<GeneSetTerm> |
GeneSetTerms.getAllChildren(GeneSetTerm term) |
Collection<GeneSetTerm> |
GeneSetTerms.getAllParents(GeneSetTerm id) |
Set<GeneSetTerm> |
GeneAnnotations.getChildren(GeneSetTerm id) |
Set<GeneSetTerm> |
GeneSetTerms.getChildren(GeneSetTerm id) |
GeneSet |
GeneAnnotations.getGeneSet(GeneSetTerm classid) |
Set<Gene> |
GeneAnnotations.getGeneSetGenes(GeneSetTerm goset) |
Set<Probe> |
GeneAnnotations.getGeneSetProbes(GeneSetTerm geneSetId) |
Double[] |
GeneScores.getGeneSetScores(GeneSetTerm geneSetTerm)
Get the gene scores for just the genes in the set indicated.
|
double |
Multifunctionality.getGOTermMultifunctionality(GeneSetTerm goId) |
double |
Multifunctionality.getGOTermMultifunctionalityPvalue(GeneSetTerm goId) |
double |
Multifunctionality.getGOTermMultifunctionalityRank(GeneSetTerm goId) |
Collection<GeneSetTerm> |
GeneSetTerms.getParents(GeneSetTerm id) |
boolean |
GeneAnnotations.hasGeneSet(GeneSetTerm id) |
boolean |
GeneAnnotations.hasRedundancy(GeneSetTerm id)
Check if a group has any redundancies.
|
boolean |
GeneAnnotations.hasUsableAspect(GeneSetTerm geneSetTerm,
boolean missingAspectTreatedAsUsable) |
boolean |
GeneSetTerms.isLeaf(GeneSetTerm id) |
boolean |
GeneSetTerms.isParent(GeneSetTerm p,
GeneSetTerm c) |
int |
GeneAnnotations.numGenesInGeneSet(GeneSetTerm id)
Get the number of genes in a gene set, identified by id.
|
int |
GeneAnnotations.numProbesInGeneSet(GeneSetTerm id)
Get the number of probes in a gene set, identified by id.
|
protected void |
Probe.removeGeneSet(GeneSetTerm t) |
boolean |
Gene.removeGeneSet(GeneSetTerm t) |
protected void |
GeneSetTerms.removeUserDefined(GeneSetTerm id) |
void |
GeneSet.setTerm(GeneSetTerm name) |
Modifier and Type | Method and Description |
---|---|
int |
GeneAnnotations.addAnnotation(Gene gene,
Collection<GeneSetTerm> terms) |
double |
Multifunctionality.correlationWithGoTermMultifunctionality(List<GeneSetTerm> rankedGoTerms) |
Collection<GeneSet> |
GeneAnnotations.getGeneSets(Collection<GeneSetTerm> terms) |
void |
Probe.setGeneSets(Collection<GeneSetTerm> geneSets) |
void |
Gene.setGeneSets(Collection<GeneSetTerm> geneSets) |
Constructor and Description |
---|
EmptyGeneSetResult(GeneSetTerm id) |
GeneSet(GeneSetTerm name) |
GeneSet(GeneSetTerm name,
Collection<Gene> items) |
GeneSetDetails(GeneSetTerm classID,
GeneAnnotations geneData,
StatusViewer callerStatusViewer)
Show without any results.
|
GeneSetDetails(GeneSetTerm classID,
GeneSetResult result,
GeneAnnotations geneData,
Settings settings,
GeneScores geneScores,
StatusViewer statusViewer)
The data matrix will be read in based on the settings, or can be changed later.
|
GeneSetResult(GeneSetTerm id,
int numProbes,
int numGenes,
double score,
double pvalue,
double correctedPvalue,
SettingsHolder settings) |
GeneSetResult(GeneSetTerm id,
int numProbes,
int numGenes,
SettingsHolder settings) |
Constructor and Description |
---|
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.
|
GeneSetTerms(Collection<GeneSetTerm> terms)
Create based only on 'user defined', without reading in GO.
|
Modifier and Type | Method and Description |
---|---|
void |
MainFrame.findGeneSetInTree(GeneSetTerm classID) |
Modifier and Type | Method and Description |
---|---|
void |
MainFrame.filter(Collection<GeneSetTerm> selectedTerms) |
Modifier and Type | Method and Description |
---|---|
GeneSetTerm |
GeneSetPanelPopupMenu.getSelectedItem() |
protected abstract GeneSetTerm |
GeneSetPanel.popupRespondAndGetGeneSet(MouseEvent e) |
Modifier and Type | Method and Description |
---|---|
protected abstract void |
GeneSetPanel.addedGeneSet(GeneSetTerm addedTerm) |
protected boolean |
GeneSetPanel.deleteUserGeneSet(GeneSetTerm classID) |
protected void |
GeneSetPanel.openUrlForGeneSet(String url,
GeneSetTerm term)
Forms a url like url + term.getId().
|
protected abstract void |
GeneSetPanel.removedGeneSet(GeneSetTerm addedTerm)
Update the view to reflect changes
|
void |
GeneSetPanelPopupMenu.setSelectedItem(GeneSetTerm selectedItem) |
protected void |
GeneSetPanel.showDetailsForGeneSet(GeneSetTerm id,
GeneSetPvalRun run)
Create the popup window with the visualization for a specific gene set and results.
|
Constructor and Description |
---|
GeneSetPanelPopupMenu(GeneSetTerm classID) |
Constructor and Description |
---|
GeneSetWizard(MainFrame callingframe,
GeneAnnotations geneData,
GeneSetTerm geneSetId)
Use this constructor when you know the gene set to be looked at, and the user doesn't have to selected it from
the list (modify a gene set).
|
Modifier and Type | Method and Description |
---|---|
protected GeneSetTerm |
GeneSetTablePanel.popupRespondAndGetGeneSet(MouseEvent e) |
Modifier and Type | Method and Description |
---|---|
void |
GeneSetTablePanel.addedGeneSet(GeneSetTerm id) |
protected boolean |
GeneSetTablePanel.deleteUserGeneSet(GeneSetTerm classID) |
protected void |
GeneSetTablePanel.removedGeneSet(GeneSetTerm addedTerm) |
Modifier and Type | Method and Description |
---|---|
void |
GeneSetTablePanel.filter(Collection<GeneSetTerm> selectedTerms) |
Modifier and Type | Field and Description |
---|---|
protected GeneSetTerm |
GeneSetTreePanel.currentlySelectedGeneSet |
Modifier and Type | Method and Description |
---|---|
GeneSetTerm |
GeneSetTreePanel.getCurrentlySelectedGeneSet() |
GeneSetTerm |
GeneSetTreeNode.getTerm() |
protected GeneSetTerm |
GeneSetTreePanel.popupRespondAndGetGeneSet(MouseEvent e) |
Modifier and Type | Method and Description |
---|---|
void |
GeneSetTreePanel.addedGeneSet(GeneSetTerm id) |
protected boolean |
GeneSetTreePanel.deleteUserGeneSet(GeneSetTerm classID) |
boolean |
GeneSetTreePanel.expandToGeneSet(GeneSetTerm classID) |
TreePath |
GeneSetTreePanel.find(GeneSetTerm id) |
protected void |
GeneSetTreePanel.removedGeneSet(GeneSetTerm id) |
Modifier and Type | Method and Description |
---|---|
void |
GeneSetTreePanel.filter(Collection<GeneSetTerm> selectedTerms) |
void |
FilteredGeneSetTreeModel.setFilterSelectedTerms(Collection<GeneSetTerm> selectedTerms) |
Constructor and Description |
---|
GeneSetTreeNode(DirectedGraphNode<String,GeneSetTerm> root) |
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