Package | Description |
---|---|
ubic.erminej.analysis | |
ubic.erminej.data | |
ubic.erminej.gui.geneset | |
ubic.erminej.gui.geneset.details | |
ubic.erminej.gui.geneset.edit | |
ubic.erminej.gui.table |
Modifier and Type | Method and Description |
---|---|
DoubleMatrix<Probe,String> |
CorrelationPvalGenerator.getData() |
Modifier and Type | Method and Description |
---|---|
boolean |
CorrelationPvalGenerator.containsRow(Probe name) |
Constructor and Description |
---|
CorrelationPvalGenerator(SettingsHolder settings,
GeneAnnotations geneAnnots,
DoubleMatrix<Probe,String> rawData,
Histogram hist,
StatusViewer messenger) |
ResamplingCorrelationGeneSetScore(SettingsHolder settings,
DoubleMatrix<Probe,String> dataMatrix) |
Modifier and Type | Method and Description |
---|---|
Probe |
GeneAnnotations.findProbe(String probe)
Case insensitive
|
Modifier and Type | Method and Description |
---|---|
Set<Probe> |
GeneAnnotations.findProbes(String searchOn)
Create a selected probes list based on a search string.
|
Collection<Probe> |
Gene.getActiveProbes() |
DoubleMatrix<Probe,String> |
GeneSetDetails.getDataMatrix() |
Set<Probe> |
GeneAnnotations.getGeneSetProbes(GeneSetTerm geneSetId) |
Set<Probe> |
GeneAnnotations.getProbes() |
Collection<Probe> |
GeneSetDetails.getProbes() |
Collection<Probe> |
Gene.getProbes() |
Set<Probe> |
GeneSet.getProbes() |
Map<Probe,Double> |
GeneSetDetails.getProbeScores()
Just for the probes in this set.
|
Map<Probe,Double> |
GeneScores.getProbeToScoreMap()
Note that these values will already be log-transformed if that was requested
|
static DoubleMatrix<Probe,String> |
DataIOUtils.readDataMatrixForAnalysis(GeneAnnotations geneAnnots,
SettingsHolder settings) |
Modifier and Type | Method and Description |
---|---|
protected void |
Gene.addProbe(Probe probe) |
boolean |
GeneAnnotations.hasProbe(Probe probeId) |
Modifier and Type | Method and Description |
---|---|
void |
Gene.setActiveProbes(Collection<Probe> activeProbes) |
void |
GeneSetDetails.setDataMatrix(DoubleMatrix<Probe,String> dm)
You only need to use this if you want to replace the matrix.
|
void |
Gene.setProbes(Collection<Probe> probes) |
GeneAnnotations |
GeneAnnotations.subClone(Collection<Probe> probesToRetain)
Create a new annotation set based on an existing one, for selected probes, removing probes with no annotations.
|
Constructor and Description |
---|
GeneAnnotations(GeneAnnotations start,
Collection<Probe> probes)
Create a read-only new annotation set based on an existing one, for selected probes, removing
probes with no annotations.
|
GeneAnnotations(GeneAnnotations start,
Collection<Probe> probes,
boolean pruneUnannotated)
Create a read-only new annotation set based on an existing one, for selected probes, optionally
removing unannotated probes.
|
Modifier and Type | Method and Description |
---|---|
List<Probe> |
ProbeTableModel.getProbes() |
Modifier and Type | Method and Description |
---|---|
void |
ProbeTableModel.addProbe(Probe p) |
void |
ProbeTableModel.removeProbe(Probe p) |
Modifier and Type | Method and Description |
---|---|
void |
ProbeTableModel.addProbes(Collection<Probe> probelist) |
void |
ProbeTableModel.removeProbes(Collection<Probe> probelist) |
void |
ProbeTableModel.setProbes(Collection<Probe> probesToUse) |
Constructor and Description |
---|
ProbeTableModel(Collection<Probe> probesToUse) |
Modifier and Type | Field and Description |
---|---|
MatrixDisplay<Probe,String> |
GeneSetDetailsFrame.matrixDisplay |
Modifier and Type | Method and Description |
---|---|
Probe |
GeneSetDetailsTableModel.getProbeAtRow(int r) |
Constructor and Description |
---|
GeneSetDetailsTableModel(MatrixDisplay<Probe,String> matrixDisplay,
GeneSetDetails geneSetDetails,
SettingsHolder settings) |
Modifier and Type | Method and Description |
---|---|
Collection<Probe> |
GeneSetWizardStep2.getProbes()
Get the results of the user's picking.
|
Constructor and Description |
---|
JMatrixCellRenderer(MatrixDisplay<Probe,String> matrixDisplay) |
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