- tearDown() - Method in class ubic.basecode.datafilter.AbstractTestFilter
-
- tearDown() - Method in class ubic.basecode.datafilter.TestRowAbsentFilter
-
- tearDown() - Method in class ubic.basecode.datafilter.TestRowNameFilter
-
- tearDown() - Method in class ubic.basecode.graphics.MatrixDisplayTest
-
- tearDown() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
-
- tearDown() - Method in class ubic.basecode.io.reader.TestMapReader
-
- tearDown() - Method in class ubic.basecode.io.TestByteArrayConverter
-
- tearDown() - Static method in class ubic.basecode.ontology.OntologyLoaderTest
-
- tearDown() - Static method in class ubic.basecode.ontology.providers.AbstractOntologyServiceTest
-
- tearDown() - Method in class ubic.basecode.util.ConfigUtilsTest
-
- tearDown() - Method in class ubic.basecode.util.FileToolsTest
-
- tearDown() - Method in class ubic.basecode.util.r.JRIClientTest
-
- tearDown() - Method in class ubic.basecode.util.r.RServeClientTest
-
- test() - Method in class ubic.basecode.dataStructure.DoubleAddingMapTest
-
- test() - Method in class ubic.basecode.dataStructure.params.ParameterKeeperTest
-
- test() - Method in class ubic.basecode.dataStructure.params.ParamGrabberTest
-
- test() - Method in class ubic.basecode.ontology.ncbo.AnnotatorClientTest
-
- test1() - Method in class ubic.basecode.math.linalg.QRDecompositionTest
-
- test2() - Method in class ubic.basecode.math.linearmodels.DesignMatrixTest
-
This matrix is singular.
- test2NoPivoting() - Method in class ubic.basecode.math.linalg.QRDecompositionTest
-
Test ability to reproduce standard QR
- test3() - Method in class ubic.basecode.math.linalg.QRDecompositionTest
-
- testA() - Method in class ubic.basecode.math.linearmodels.DesignMatrixTest
-
- testAddChild() - Method in class ubic.basecode.dataStructure.graph.TestDirectedGraph
-
- testAddChildFail() - Method in class ubic.basecode.dataStructure.graph.TestDirectedGraph
-
- testAddDataExtension() - Method in class ubic.basecode.util.FileToolsTest
-
- testAddImageExtension() - Method in class ubic.basecode.util.FileToolsTest
-
- testAddParent() - Method in class ubic.basecode.dataStructure.graph.TestDirectedGraph
-
- testAddParentFail() - Method in class ubic.basecode.dataStructure.graph.TestDirectedGraph
-
- testAddrow() - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrixTest
-
- testAExact() - Method in class ubic.basecode.math.TestWilcoxon
-
- testAnovaA() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
- testAnovaB() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
- testAnovaC() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
- testAnovaD() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
- testAnovaE() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
- testAnovaF() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
One way @
- testAroc() - Method in class ubic.basecode.math.TestROC
-
- testArocPvalue() - Method in class ubic.basecode.math.TestROC
-
- testArray - Variable in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testAssign() - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1DTest
-
- testAssignAndRetrieveMatrix() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
- testAssignAndRetrieveMatrixB() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
- testAssignAndRetrieveMatrixC() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
- testAssignAndRetrieveMatrixD() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
- testAssignAr() - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1DTest
-
- testAssignDoubleFunction() - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1DTest2
-
- testAssignStringList() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
- testAutoCorrelation() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testAveragePrecision() - Method in class ubic.basecode.math.PrecisionRecallTest
-
- testAveragePrecisionB() - Method in class ubic.basecode.math.PrecisionRecallTest
-
- testAveragePrecisionBNotInOrder() - Method in class ubic.basecode.math.PrecisionRecallTest
-
- testAveragePrecisionNotInOrder() - Method in class ubic.basecode.math.PrecisionRecallTest
-
- testAveragePrecisionWithTie() - Method in class ubic.basecode.math.PrecisionRecallTest
-
Should give the same result as test B, because precision is the same at each step despite the tie.
- testB() - Method in class ubic.basecode.math.linearmodels.DesignMatrixTest
-
- testB() - Method in class ubic.basecode.ontology.ncbo.AnnotatorClientTest
-
- testBadFileName() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
-
- testBadMatch() - Method in class ubic.basecode.math.StringDistanceTest
-
- testBatches() - Method in class ubic.basecode.util.BatchIteratorTest
-
Test method for ca.elmonline.util.BatchIterator#batches(java.util.Collection, int).
- testBatchIterator() - Method in class ubic.basecode.util.BatchIteratorTest
-
Test method for ca.elmonline.util.BatchIterator#BatchIterator(java.util.Collection, int).
- testBenjaminiHochberg() - Method in class ubic.basecode.math.MultipleTestCorrectionTest
-
- testBenjaminiHochbergCut() - Method in class ubic.basecode.math.MultipleTestCorrectionTest
-
- testBenjaminiHochbergM() - Method in class ubic.basecode.math.MultipleTestCorrectionTest
-
- testBenjaminiYekuteliCut() - Method in class ubic.basecode.math.MultipleTestCorrectionTest
-
- testBGaussian() - Method in class ubic.basecode.math.TestWilcoxon
-
- testBig() - Method in class ubic.basecode.math.TestROC
-
Bug 3620
- testBig() - Method in class ubic.basecode.math.TestWilcoxon
-
- testBitCount() - Method in class ubic.basecode.dataStructure.matrix.CompressedNamedBitMatrixTest
-
- testBitMatrix() - Method in class ubic.basecode.dataStructure.matrix.CompressedNamedBitMatrixTest
-
- testBlobToString() - Method in class ubic.basecode.util.SQLUtilsTest
-
- testBonferroniCut() - Method in class ubic.basecode.math.MultipleTestCorrectionTest
-
- testBooleansToByteArray() - Method in class ubic.basecode.io.TestByteArrayConverter
-
- testBooleansToLongArray() - Method in class ubic.basecode.io.TestByteArrayConverter
-
- TestByteArrayConverter - Class in ubic.basecode.io
-
- TestByteArrayConverter() - Constructor for class ubic.basecode.io.TestByteArrayConverter
-
- testByteArrayToBooleans() - Method in class ubic.basecode.io.TestByteArrayConverter
-
- testByteArrayToDoubleConversionSpeed() - Method in class ubic.basecode.io.TestByteArrayConverter
-
- testByteArrayToDoubleMatrix() - Method in class ubic.basecode.io.TestByteArrayConverter
-
- testByteArrayToDoubles() - Method in class ubic.basecode.io.TestByteArrayConverter
-
- testByteArrayToLongs() - Method in class ubic.basecode.io.TestByteArrayConverter
-
- testByteArrayToTabbedString() - Method in class ubic.basecode.io.TestByteArrayConverter
-
- testC() - Method in class ubic.basecode.ontology.ncbo.AnnotatorClientTest
-
- testCacheOntologyToDisk() - Method in class ubic.basecode.ontology.providers.AbstractOntologyServiceTest
-
- testCdf() - Method in class ubic.basecode.math.TestStats
-
- testCGaussian() - Method in class ubic.basecode.math.TestWilcoxon
-
- testChangeExtension() - Method in class ubic.basecode.util.FileToolsTest
-
- testCheckForFile() - Method in class ubic.basecode.util.NetUtilsTest
-
- testCheckPathIsReadableFile() - Method in class ubic.basecode.util.FileToolsTest
-
- testCheckPathIsReadableFileNot() - Method in class ubic.basecode.util.FileToolsTest
-
- testChooseRandomDeck() - Method in class ubic.basecode.math.RandomChooserTest
-
- testChooserandomInt() - Method in class ubic.basecode.math.RandomChooserTest
-
- testChooserandomInts() - Method in class ubic.basecode.math.RandomChooserTest
-
- testChooserandomWrep() - Method in class ubic.basecode.math.RandomChooserTest
-
- testCleanFileName() - Method in class ubic.basecode.util.FileToolsTest
-
- testCleanFileNameErr() - Method in class ubic.basecode.util.FileToolsTest
-
- testClear() - Method in class ubic.basecode.dataStructure.BitUtilTest
-
- testColSumsWithMissing() - Method in class ubic.basecode.math.TestMatrixStats
-
- testColumns() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testColumns() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
-
- testColumns() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
-
- testColumns() - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrixTest
-
- testCommonPrefix() - Method in class ubic.basecode.util.StringUtilTest
-
- testCommonPrefixNone() - Method in class ubic.basecode.util.StringUtilTest
-
- testCommonSuffix() - Method in class ubic.basecode.util.StringUtilTest
-
- testCommonSuffixNone() - Method in class ubic.basecode.util.StringUtilTest
-
- testConcurrentModificationException() - Method in class ubic.basecode.util.BatchIteratorTest
-
- testConstructFromArray() - Method in class ubic.basecode.dataStructure.matrix.DenseDoubleMatrixTest
-
- testConstructFromArray() - Method in class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrixTest
-
- testConvertLog() - Method in class ubic.basecode.math.TestMatrixStats
-
- testConvertToLog2Cpm() - Method in class ubic.basecode.math.TestMatrixStats
-
- testCopy() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testCopy() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
-
- testCopyFile() - Method in class ubic.basecode.util.FileToolsTest
-
- testCopyFileFailOnDirectoryInput() - Method in class ubic.basecode.util.FileToolsTest
-
- testCopyFileFailOnDirectoryOutput() - Method in class ubic.basecode.util.FileToolsTest
-
- testCorrel() - Method in class ubic.basecode.math.CorrelationStatsTest
-
- testCorrelAsByte() - Method in class ubic.basecode.math.CorrelationStatsTest
-
- testCorrelationA() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testCorrelationB() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- TestCorrelationEffectMetaAnalysis - Class in ubic.basecode.math.metaanalysis
-
Tests based on Cooper and Hedges.
- TestCorrelationEffectMetaAnalysis() - Constructor for class ubic.basecode.math.metaanalysis.TestCorrelationEffectMetaAnalysis
-
- testCorrelationForPvalue() - Method in class ubic.basecode.math.CorrelationStatsTest
-
- testCorrelationMatrix() - Method in class ubic.basecode.math.TestMatrixStats
-
- testCorrelationMatrixThreshold() - Method in class ubic.basecode.math.TestMatrixStats
-
- testCorrelationOfStandardizedDoubleArrayDoubleArray() - Method in class ubic.basecode.math.DistanceTest
-
- testCorrelationOfStandardizedDoubleArrayListDoubleArrayList() - Method in class ubic.basecode.math.DistanceTest
-
- testCorrelTooSmall() - Method in class ubic.basecode.math.CorrelationStatsTest
-
- testCount() - Method in class ubic.basecode.dataStructure.BitUtilTest
-
- testCount() - Method in class ubic.basecode.dataStructure.CountingMapTest
-
Test method for ca.elmonline.util.CountingMap#count(java.lang.Object).
- testCountsPerMillionWithMissing() - Method in class ubic.basecode.math.TestMatrixStats
-
- testCov2Cor() - Method in class ubic.basecode.math.TestMatrixStats
-
- testCovariance() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testCsvSplitA() - Method in class ubic.basecode.util.TestStringUtil
-
- testCsvSplitB() - Method in class ubic.basecode.util.TestStringUtil
-
- testCsvSplitC() - Method in class ubic.basecode.util.TestStringUtil
-
- testCsvSplitD() - Method in class ubic.basecode.util.TestStringUtil
-
- testCsvSplitE() - Method in class ubic.basecode.util.TestStringUtil
-
- testCsvSplitF() - Method in class ubic.basecode.util.TestStringUtil
-
- testCumHyperGeometric() - Method in class ubic.basecode.math.TestSpecFunc
-
- testCumHyperGeometricB() - Method in class ubic.basecode.math.TestSpecFunc
-
- testCumHyperGeometricUT() - Method in class ubic.basecode.math.TestSpecFunc
-
- testCumulate() - Method in class ubic.basecode.math.TestStats
-
- testCumulateRight() - Method in class ubic.basecode.math.TestStats
-
- testCv() - Method in class ubic.basecode.math.TestStats
-
- testdata - Variable in class ubic.basecode.datafilter.AbstractTestFilter
-
- testdata - Variable in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testdata - Variable in class ubic.basecode.math.TestMatrixRowStats
-
- testDataFrameA() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
- testdBinom() - Method in class ubic.basecode.math.TestSpecFunc
-
- testDeleteDir() - Method in class ubic.basecode.util.FileToolsTest
-
Tests trying to delete a directory without first deleting the files.
- testDeleteFilesAndDir() - Method in class ubic.basecode.util.FileToolsTest
-
Tests deleting files in a directory tree, then the directories.
- testDeleteLeaf1() - Method in class ubic.basecode.dataStructure.graph.TestDirectedGraph
-
- testDeleteLeafFail() - Method in class ubic.basecode.dataStructure.graph.TestDirectedGraph
-
- testDeleteLeafNotLeaf() - Method in class ubic.basecode.dataStructure.graph.TestDirectedGraph
-
- testDensity() - Method in class ubic.basecode.math.distribution.UniformDensityComputerTest
-
- TestDescriptiveWithMissing - Class in ubic.basecode.math
-
- TestDescriptiveWithMissing() - Constructor for class ubic.basecode.math.TestDescriptiveWithMissing
-
- TestDirectedGraph - Class in ubic.basecode.dataStructure.graph
-
- TestDirectedGraph() - Constructor for class ubic.basecode.dataStructure.graph.TestDirectedGraph
-
- testDoubleArrayToByteArrayConversionSpeed() - Method in class ubic.basecode.io.TestByteArrayConverter
-
- testDoubleArrayToBytes() - Method in class ubic.basecode.io.TestByteArrayConverter
-
- testDoubleArrayToDelimitedStringConversionSpeed() - Method in class ubic.basecode.io.TestByteArrayConverter
-
- testDoubleArrayTwoDoubleArrayEval() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
- TestDoubleMatrixReader - Class in ubic.basecode.io.reader
-
- TestDoubleMatrixReader() - Constructor for class ubic.basecode.io.reader.TestDoubleMatrixReader
-
- testDoubleStandardize() - Method in class ubic.basecode.math.TestMatrixStats
-
- testDoubleTwoDoubleArrayEval() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
- testDownloadFile() - Method in class ubic.basecode.util.NetUtilsTest
-
- testDropColumn() - Method in class ubic.basecode.dataStructure.matrix.MatrixUtilTest
-
- testDuplicateRows() - Method in class ubic.basecode.math.linearmodels.MeanVarianceEstimatorTest
-
Duplicate row
- testDurbinWatson() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testDurbinWatsonShort() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testDurbinWatsonTwo() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testDVolume() - Method in class ubic.basecode.math.TestWilcoxon
-
- testEditDistanceA() - Method in class ubic.basecode.math.StringDistanceTest
-
- testEditDistanceB() - Method in class ubic.basecode.math.StringDistanceTest
-
- testEditDistanceC() - Method in class ubic.basecode.math.StringDistanceTest
-
- testEditDistanceD() - Method in class ubic.basecode.math.StringDistanceTest
-
- testEditDistanceE() - Method in class ubic.basecode.math.StringDistanceTest
-
- testEditDistanceF() - Method in class ubic.basecode.math.StringDistanceTest
-
- testEditDistanceG() - Method in class ubic.basecode.math.StringDistanceTest
-
- testEditDistanceH() - Method in class ubic.basecode.math.StringDistanceTest
-
- testEstrogen() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
-
Tests limma-like functionality.
- testEuclDistance() - Method in class ubic.basecode.math.DistanceTest
-
- testEVolume() - Method in class ubic.basecode.math.TestWilcoxon
-
- testExec() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
- testExecDoubleArray() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
- testExecError() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
- testExpandedSize() - Method in class ubic.basecode.dataStructure.StringToStringSetMapTest
-
- testExpandedValues() - Method in class ubic.basecode.dataStructure.StringToStringSetMapTest
-
- testFactorAssign() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
- testFdist() - Method in class ubic.basecode.math.linearmodels.ModeratedTstatTest
-
- testFillRange() - Method in class ubic.basecode.math.TestMathUtil
-
- testFillRangeDown() - Method in class ubic.basecode.math.TestMathUtil
-
- testFillRangeNo() - Method in class ubic.basecode.math.TestMathUtil
-
- testFilter() - Method in class ubic.basecode.datafilter.TestItemLevelFilter
-
- testFilter() - Method in class ubic.basecode.datafilter.TestRowAbsentFilter
-
- testFilter() - Method in class ubic.basecode.datafilter.TestRowAffyNameFilter
-
- testFilter() - Method in class ubic.basecode.datafilter.TestRowMissingFilter
-
- testFilter() - Method in class ubic.basecode.datafilter.TestRowNameFilter
-
- testFilterBadFraction() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
-
- testFilterExclude() - Method in class ubic.basecode.datafilter.TestRowNameFilter
-
- testFilterFraction() - Method in class ubic.basecode.datafilter.TestRowAbsentFilter
-
- testFilterFraction() - Method in class ubic.basecode.datafilter.TestRowMissingFilter
-
- testFilterFractionInvalid() - Method in class ubic.basecode.datafilter.TestRowAbsentFilter
-
- testFilterFractionInvalid() - Method in class ubic.basecode.datafilter.TestRowMissingFilter
-
- testFilterFractionInvalid2() - Method in class ubic.basecode.datafilter.TestRowMissingFilter
-
- testFilterFractionMaxRemoveHighAndLow() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
-
- testFilterFractionMaxRemoveHighAndLowBothFraction() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
-
- testFilterFractionMaxRemoveHighAndLowBothLevels() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
-
- testFilterFractionMaxRemoveHighAndLowBothLevelsNegLow() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
-
- testFilterFractionMaxRemoveHighAndLowBothLevelsNoNegRemove() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
-
- testFilterFractionMaxRemoveNeg() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
-
- testFilterFractionMaxRemoveNegHigh() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
-
- testFilterKeepMarginal() - Method in class ubic.basecode.datafilter.TestRowAbsentFilter
-
- testfilterlist - Variable in class ubic.basecode.datafilter.TestRowNameFilter
-
- testFilterMax() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
-
- testFilterMaxFraction() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
-
- testFilterMaxFractionAll() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
-
- testFilterMaxFractionHigh() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
-
- testFilterMaxFractionNone() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
-
- testFilterMaxFractionNoneRemoveNeg() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
-
- testFilterMaxHigh() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
-
- testFilterMaxTooHigh() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
-
- testFilterMean() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
-
- testFilterMeanHigh() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
-
- testFilterMedian() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
-
mm<-read.table("testdata.txt", header=T, row.names=1)
length(which(apply(mm, 1, median) > 100))
- testFilterMedianHigh() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
-
mm<-read.table("testdata.txt", header=T, row.names=1)
length(which(apply(mm, 1, median) < 1000))
- testFilterMin() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
-
- testFilterMinHigh() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
-
- testFilterNoFilter() - Method in class ubic.basecode.datafilter.TestRowLevelFilter
-
- testFilterNoFiltering() - Method in class ubic.basecode.datafilter.TestRowMissingFilter
-
- testFilterNullFlags() - Method in class ubic.basecode.datafilter.TestRowAbsentFilter
-
- testFilterPresentCountInvalid() - Method in class ubic.basecode.datafilter.TestRowAbsentFilter
-
- testFilterPresentCountInvalid() - Method in class ubic.basecode.datafilter.TestRowMissingFilter
-
- testFilterString() - Method in class ubic.basecode.datafilter.TestRowNameFilter
-
- testFilterStringExclude() - Method in class ubic.basecode.datafilter.TestRowNameFilter
-
- testFilterStringMatrix() - Method in class ubic.basecode.datafilter.TestRowAbsentFilter
-
- testFilterStringMatrix() - Method in class ubic.basecode.datafilter.TestRowMissingFilter
-
- testFilterWithMissing() - Method in class ubic.basecode.datafilter.TestRowAbsentFilter
-
- testFilterWithMissing() - Method in class ubic.basecode.datafilter.TestRowMissingFilter
-
- testFilterWithMissingLessStringent() - Method in class ubic.basecode.datafilter.TestRowAbsentFilter
-
- testFilterWithMissingLessStringent() - Method in class ubic.basecode.datafilter.TestRowMissingFilter
-
- testFilterWithMissingLowMaxFraction() - Method in class ubic.basecode.datafilter.TestRowMissingFilter
-
- testFindExecutable() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
- testFisherCombinePvalues() - Method in class ubic.basecode.math.metaanalysis.MetaAnalysisTest
-
- testFisherCombinePvaluesB() - Method in class ubic.basecode.math.metaanalysis.MetaAnalysisTest
-
- testFtpFileSize() - Method in class ubic.basecode.util.NetUtilsTest
-
- testFtpFileSizeDoesntExist() - Method in class ubic.basecode.util.NetUtilsTest
-
- testFVolume() - Method in class ubic.basecode.math.TestWilcoxon
-
- testGenericOntologyServiceMem() - Method in class ubic.basecode.ontology.providers.AbstractOntologyServiceTest
-
- testGeometricMean() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testGet() - Method in class ubic.basecode.dataStructure.BitUtilTest
-
- testGet() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testGet() - Method in class ubic.basecode.dataStructure.matrix.CompressedNamedBitMatrixTest
-
- testget() - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrixTest
-
- testGet() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
-
- testGet() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
-
- testGet2() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testGetApproximateQuantile() - Method in class ubic.basecode.math.distribution.HistogramTest
-
- testGetBiggestBinSize() - Method in class ubic.basecode.math.distribution.HistogramTest
-
- testGetByKeys() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testGetByKeys() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
-
- testGetByKeys() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
-
- testGetChildren() - Method in class ubic.basecode.dataStructure.graph.TestDirectedGraph
-
- testGetChildren() - Method in class ubic.basecode.ontology.OntologyTermTest
-
- testGetChildrenHasProperPart() - Method in class ubic.basecode.ontology.OntologyTermTest
-
FIXME this uses NIF, which we are no longer using actively - not a big deal since this just tests mechanics
- testGetColByName() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testGetColByName() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
-
Test method for ubic.basecode.dataStructure.matrix.SparseDoubleMatrix#getColByName(java.lang.Object).
- testGetColByNameFail() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testGetColByNameNull() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testGetColObj() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testgetcolobj() - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrixTest
-
- testGetColObj() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
-
- testGetColObj() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
-
- testGetColObj() - Method in class ubic.basecode.dataStructure.matrix.StringMatrixTest
-
- testGetColObj2() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testGetColRange() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testGetColRange() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
-
- testGetColRange() - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrixTest
-
- testGetColumn() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testGetColumn() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
-
- testGetColumn() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
-
- testGetCompressedFile() - Method in class ubic.basecode.util.FileToolsTest
-
- testGetCompressedFileZip() - Method in class ubic.basecode.util.FileToolsTest
-
- testGetConfigBuilderFile() - Method in class ubic.basecode.util.ConfigUtilsTest
-
- testGetConfigBuilderFileNew() - Method in class ubic.basecode.util.ConfigUtilsTest
-
- testGetConfigBuilderString() - Method in class ubic.basecode.util.ConfigUtilsTest
-
- testGetConfigBuilderStringNew() - Method in class ubic.basecode.util.ConfigUtilsTest
-
- testGetConfigBuilderURL() - Method in class ubic.basecode.util.ConfigUtilsTest
-
- testGetConfigBuilderURLNew() - Method in class ubic.basecode.util.ConfigUtilsTest
-
- testGetEntry() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
-
- testGetExtension() - Method in class ubic.basecode.util.FileToolsTest
-
- testGetInputStreamFromPlainOrCompressedFile() - Method in class ubic.basecode.util.FileToolsTest
-
- testGetLeft() - Method in class ubic.basecode.dataStructure.tree.BinaryTreeTest
-
Test method for ubic.basecode.dataStructure.tree.BinaryTree#getLeft().
- testGetLines() - Method in class ubic.basecode.util.FileToolsTest
-
- testGetObject() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testGetObject() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
-
- testGetObject() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
-
- testGetOutOfBounds() - Method in class ubic.basecode.dataStructure.matrix.CompressedNamedBitMatrixTest
-
- testGetParents() - Method in class ubic.basecode.ontology.OntologyTermTest
-
- testGetParentsHasProperPart() - Method in class ubic.basecode.ontology.OntologyTermTest
-
- testgetRelative5yearsago() - Method in class ubic.basecode.util.DateUtilTest
-
- testgetRelative5yearsFromnow() - Method in class ubic.basecode.util.DateUtilTest
-
- testgetRelativeDateDayago() - Method in class ubic.basecode.util.DateUtilTest
-
- testgetRelativeTomorrow() - Method in class ubic.basecode.util.DateUtilTest
-
- testGetRight() - Method in class ubic.basecode.dataStructure.tree.BinaryTreeTest
-
Test method for ubic.basecode.dataStructure.tree.BinaryTree#getRight().
- testGetRoot() - Method in class ubic.basecode.dataStructure.tree.BinaryTreeTest
-
- testGetRow() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testGetRow() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
-
- testGetRow() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
-
- testGetRow() - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrixTest
-
- testGetRow2() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testGetRowArrayList() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testGetRowArrayList() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
-
- testGetRowArrayList() - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrixTest
-
- testGetRowArrayList2() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testGetRowBitCount() - Method in class ubic.basecode.dataStructure.matrix.CompressedNamedBitMatrixTest
-
- testGetRowByName() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testGetRowByName() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
-
- testGetRowByNameFail() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testGetRowByNameNull() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testGetRowMatrix1D() - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrixTest
-
- testGetRowObj() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testgetrowobj() - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrixTest
-
- testGetRowObj() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
-
- testGetRowObj() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
-
- testGetRowObj2() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testGetRowRange() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testGetRowRange() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
-
- testGetRowRange() - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrixTest
-
- testGetSet() - Method in class ubic.basecode.io.excel.ExcelUtilTest
-
- testGetSheetFromFile() - Method in class ubic.basecode.io.excel.ExcelUtilTest
-
- testgetStringListFromFile() - Method in class ubic.basecode.util.FileToolsTest
-
- testGetWithoutExtension() - Method in class ubic.basecode.util.FileToolsTest
-
- testGetWithoutExtensionB() - Method in class ubic.basecode.util.FileToolsTest
-
- testGetWithoutExtensionC() - Method in class ubic.basecode.util.FileToolsTest
-
- testHammingDistance() - Method in class ubic.basecode.math.StringDistanceTest
-
- testHasImageExtension() - Method in class ubic.basecode.util.FileToolsTest
-
- testHasXMLExtension() - Method in class ubic.basecode.util.FileToolsTest
-
- testHistogramReaderIs() - Method in class ubic.basecode.io.reader.HistogramReaderTest
-
- testHistogramReaderString() - Method in class ubic.basecode.io.reader.HistogramReaderTest
-
- TestHistogramWriter - Class in ubic.basecode.io.writer
-
- TestHistogramWriter() - Constructor for class ubic.basecode.io.writer.TestHistogramWriter
-
- testHypergeometric() - Method in class ubic.basecode.math.TestSpecFunc
-
- testIncrement() - Method in class ubic.basecode.dataStructure.CountingMapTest
-
Test method for ca.elmonline.util.CountingMap#increment(java.lang.Object).
- testIncrementalUpdate() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testIncrementalUpdateSums() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testIncrementalWeightedUpdate() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testIndexing() - Method in class ubic.basecode.ontology.search.OntologySearchTest
-
- testInsertLeft() - Method in class ubic.basecode.dataStructure.tree.BinaryTreeTest
-
- testInsertRight() - Method in class ubic.basecode.dataStructure.tree.BinaryTreeTest
-
- testInteractionAndRelevel() - Method in class ubic.basecode.math.linearmodels.DesignMatrixTest
-
- testInteractionC() - Method in class ubic.basecode.math.linearmodels.DesignMatrixTest
-
- testInterpolate() - Method in class ubic.basecode.math.linearmodels.MeanVarianceEstimatorTest
-
Tests two things: 1.
- testIntsToBytes() - Method in class ubic.basecode.io.TestByteArrayConverter
-
- testInvalidVariance() - Method in class ubic.basecode.math.distribution.NormalProbabilityComputerTest
-
- testInverseFisherTransform() - Method in class ubic.basecode.math.CorrelationStatsTest
-
- testIsEmpty() - Method in class ubic.basecode.dataStructure.tree.BinaryTreeTest
-
- testIsGZipped() - Method in class ubic.basecode.util.FileToolsTest
-
- testIsLeaf() - Method in class ubic.basecode.dataStructure.tree.BinaryTreeTest
-
- testIsMissing() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testIsMissing() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
-
- testIsMissing() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
-
- testIsMissing2() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testIsValidFraction() - Method in class ubic.basecode.math.TestStats
-
- testIsValidFraction2() - Method in class ubic.basecode.math.TestStats
-
- testIsZipped() - Method in class ubic.basecode.util.FileToolsTest
-
- TestItemLevelFilter - Class in ubic.basecode.datafilter
-
- TestItemLevelFilter() - Constructor for class ubic.basecode.datafilter.TestItemLevelFilter
-
- TestKSTest - Class in ubic.basecode.math
-
- TestKSTest() - Constructor for class ubic.basecode.math.TestKSTest
-
- testKSTestOneSample() - Method in class ubic.basecode.math.TestKSTest
-
- testKSTestTwoSample() - Method in class ubic.basecode.math.TestKSTest
-
- testKurtosis() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testKurtosisList() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testKW() - Method in class ubic.basecode.math.KruskalWallisTest
-
- testLag1() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testLimma() - Method in class ubic.basecode.math.linearmodels.ModeratedTstatTest
-
- testLimmaA() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
Also exercises dataFrameEval
library(limma)
dat<-read.table("data/testdata.txt", header=T, row.names=1)
f1<-factor(c("A", "A", "A", "A", "A", "A", "B", "B", "B", "B", "B", "B"));
f2<-factor(c("X", "X", "Y", "Y", "Z", "Z", "X", "X", "Y", "Y", "Z", "Z"));
cov1<-c( -0.230 , 1.400, -0.210, 0.570, -0.064, 0.980 ,-0.082, -0.094, 0.630, -2.000, 0.640, -0.870);
mo<-model.matrix(˜ f1 + f2 + cov1 - 1);
contr<-makeContrasts(A-B, levels=mo);
fit<-lmFit(dat, mo);
fit<-contrasts.fit(fit, contr);
fit<-eBayes(fit)
res<-topTable(fit)
- testLimmaMissing() - Method in class ubic.basecode.math.linearmodels.ModeratedTstatTest
-
- testLinearModelA() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
Like a two-sample t-test where the intercept is also of interest
- testLinearModelB() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
With a continuous covariate as well a categorical one
- testLinearModelC() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
- testLinearModelD() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
Basically a one-way anova with 4 levels in the factor
- testListDirectoryFiles() - Method in class ubic.basecode.util.FileToolsTest
-
- testListEvalA() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
- testListEvalB() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
- testLoadAndSearch() - Method in class ubic.basecode.ontology.providers.ObiServiceTest
-
- testLoadConfigFile() - Method in class ubic.basecode.util.ConfigUtilsTest
-
- testLoadConfigFileNew() - Method in class ubic.basecode.util.ConfigUtilsTest
-
- testLoadConfigString() - Method in class ubic.basecode.util.ConfigUtilsTest
-
- testLoadConfigStringNew() - Method in class ubic.basecode.util.ConfigUtilsTest
-
- testLoadConfigStringNewName() - Method in class ubic.basecode.util.ConfigUtilsTest
-
- testLoadConfigURL() - Method in class ubic.basecode.util.ConfigUtilsTest
-
- testLoadConfigURLNew() - Method in class ubic.basecode.util.ConfigUtilsTest
-
- testLoadLibrary() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
- testLoadScript() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
- testLogTransform() - Method in class ubic.basecode.math.TestMatrixStats
-
- testLSFOneContinuousWithMissing3() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
-
- testLSFThreeLevelsOnecontinous2() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
-
- testLSFThreeLevelsOneContinuousWithMissing3() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
-
- testLSFTwoLevels() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
-
- testLSFTwoLevels2() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
-
Many missing values; Two factors, two levels + interaction.
- testLSFTwoLevels3() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
-
- testLSFTwoLevelsOneContinuous() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
-
- testM - Variable in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testMad() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testMakeRnames() - Method in class ubic.basecode.util.StringUtilTest
-
- testManhattanDistance() - Method in class ubic.basecode.math.DistanceTest
-
- TestMapReader - Class in ubic.basecode.io.reader
-
- TestMapReader() - Constructor for class ubic.basecode.io.reader.TestMapReader
-
- TestMathUtil - Class in ubic.basecode.math
-
- TestMathUtil() - Constructor for class ubic.basecode.math.TestMathUtil
-
- testMatrix() - Method in class ubic.basecode.dataStructure.StringToStringSetMapTest
-
- testMatrix2() - Method in class ubic.basecode.dataStructure.StringToStringSetMapTest
-
- TestMatrixNormalizer - Class in ubic.basecode.math
-
- TestMatrixNormalizer() - Constructor for class ubic.basecode.math.TestMatrixNormalizer
-
- TestMatrixRowStats - Class in ubic.basecode.math
-
- TestMatrixRowStats() - Constructor for class ubic.basecode.math.TestMatrixRowStats
-
- TestMatrixStats - Class in ubic.basecode.math
-
- TestMatrixStats() - Constructor for class ubic.basecode.math.TestMatrixStats
-
- testMatrixWeightedMeanVariance() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest2
-
Weighted regression test - Based on a few genes from GSE9376, but samples scrambled
- testMatrixWeightedRegress() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
-
Weighted least squares test for 2D matrices
- testMax() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testMax() - Method in class ubic.basecode.math.TestMathUtil
-
- testMax() - Method in class ubic.basecode.math.TestMatrixStats
-
- testMaxFractionRemovedInvalid() - Method in class ubic.basecode.datafilter.TestRowMissingFilter
-
- testMean() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testMeanAboveQuantile() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testMeanAboveQuantile() - Method in class ubic.basecode.math.TestStats
-
- TestMeanDifferenceMetaAnalysis - Class in ubic.basecode.math.metaanalysis
-
- TestMeanDifferenceMetaAnalysis() - Constructor for class ubic.basecode.math.metaanalysis.TestMeanDifferenceMetaAnalysis
-
- testMeanDoubleAr() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testMeanDoubleArB() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testMeanEff() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testMeans() - Method in class ubic.basecode.math.TestMatrixRowStats
-
- testMeans2() - Method in class ubic.basecode.math.TestMatrixRowStats
-
- testMeanVarianceNoDesignWithColsRowAllMissing() - Method in class ubic.basecode.math.linearmodels.MeanVarianceEstimatorTest
-
Data has missing values, no Design matrix provided so plot a generic mean-variance plot
- testMeanVarianceNoDesignWithMissing() - Method in class ubic.basecode.math.linearmodels.MeanVarianceEstimatorTest
-
Data has missing values, no Design matrix provided so plot a generic mean-variance plot (no voom)
- testMedian() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testMin() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testMin() - Method in class ubic.basecode.math.TestMatrixStats
-
- testmissingdata - Variable in class ubic.basecode.datafilter.AbstractTestFilter
-
- testNan() - Method in class ubic.basecode.math.TestMatrixStats
-
- testNextDoubleMatrix() - Method in class ubic.basecode.math.distribution.TestWishart
-
- testNextSample() - Method in class ubic.basecode.math.distribution.HistogramSamplerTest
-
- testNHBE() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
-
Tests limma-like functionality
Multiple levels per factor, unbalanced design
- testNormalizeDoubleArrayList() - Method in class ubic.basecode.math.TestStats
-
- testNormalizeDoubleArrayListdouble() - Method in class ubic.basecode.math.TestStats
-
- testNumberOfDistinctValues() - Method in class ubic.basecode.math.TestStats
-
- testNumberOfDistinctValuesNonNA() - Method in class ubic.basecode.math.TestStats
-
- testObjectToBytes() - Method in class ubic.basecode.io.TestByteArrayConverter
-
- testOmitBadPredicates() - Method in class ubic.basecode.ontology.search.OntologySearchTest
-
See bug 2920
- testOmitBadPredicates2() - Method in class ubic.basecode.ontology.search.OntologySearchTest
-
See bug 3269
- testOmitDefinitions() - Method in class ubic.basecode.ontology.search.OntologySearchTest
-
- testOmitDefinitions2() - Method in class ubic.basecode.ontology.search.OntologySearchTest
-
- testOmitDefinitions3() - Method in class ubic.basecode.ontology.search.OntologySearchTest
-
- testOmitDefinitions4() - Method in class ubic.basecode.ontology.search.OntologySearchTest
-
- testOneWayAnova() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
-
Has a lot of missing values.
- testOptimizedCorrelation() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testOrder() - Method in class ubic.basecode.math.TestRank
-
- testOrderB() - Method in class ubic.basecode.math.TestRank
-
- testOutOfBounds() - Method in class ubic.basecode.dataStructure.matrix.CompressedNamedBitMatrixTest
-
- testOutOfBounds2() - Method in class ubic.basecode.dataStructure.matrix.CompressedNamedBitMatrixTest
-
- testOverlap() - Method in class ubic.basecode.dataStructure.matrix.CompressedNamedBitMatrixTest
-
- testPersistence() - Method in class ubic.basecode.ontology.search.OntologySearchTest
-
- testPrintBeans() - Method in class ubic.basecode.util.PrettyPrinterTest
-
- testProbabilityDouble() - Method in class ubic.basecode.math.distribution.NormalProbabilityComputerTest
-
- testProbabilityDoubleBoolean() - Method in class ubic.basecode.math.distribution.NormalProbabilityComputerTest
-
- testProbabilityDoubleBooleanLower() - Method in class ubic.basecode.math.distribution.NormalProbabilityComputerTest
-
- testProduct() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testPvalue() - Method in class ubic.basecode.math.CorrelationStatsTest
-
- testQuantile() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testQuantile() - Method in class ubic.basecode.math.TestStats
-
- testQuantile75() - Method in class ubic.basecode.math.TestStats
-
- testQuantileInverse() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testQuantileNormalize() - Method in class ubic.basecode.math.TestMatrixNormalizer
-
mm<-read.table("testdata.txt", header=T, row.names=1)
library(preprocessCore)
rr<-normalize.quantiles(as.matrix(mm))
rr[3,5]
[1] 29860.93
> rr[13,5]
[1] 466.7833
> rr[3,12]
[1] 31620.79
> rr[4,10]
[1] 1071.525
> rr[6,7]
[1] 288.925
>
- testQuantileNormalizeWithMissing() - Method in class ubic.basecode.math.TestMatrixNormalizer
-
Note that we do this differnetly than the Bioconductor implementation.
- testQuantiles() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testRandomSubset() - Method in class ubic.basecode.math.RandomChooserTest
-
- testRange() - Method in class ubic.basecode.math.TestStats
-
- testRange() - Method in class ubic.basecode.util.DateUtilTest
-
- testRangeBad() - Method in class ubic.basecode.util.DateUtilTest
-
- TestRank - Class in ubic.basecode.math
-
- TestRank() - Constructor for class ubic.basecode.math.TestRank
-
- testRankInterpolated() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testRankTransformDoubleArrayList() - Method in class ubic.basecode.math.TestRank
-
- testRankTransformDoubleArrayListDesc() - Method in class ubic.basecode.math.TestRank
-
- testRankTransformMap() - Method in class ubic.basecode.math.TestRank
-
- testRankTransformMapDesc() - Method in class ubic.basecode.math.TestRank
-
- testRankWithTies() - Method in class ubic.basecode.math.TestRank
-
- testRankWithTiesB() - Method in class ubic.basecode.math.TestRank
-
- testRankWithTiesC() - Method in class ubic.basecode.math.TestRank
-
- testRankWithTiesD() - Method in class ubic.basecode.math.TestRank
-
- testRankWithTiesE() - Method in class ubic.basecode.math.TestRank
-
- testRbfNormalize() - Method in class ubic.basecode.math.TestMatrixStats
-
- testRead() - Method in class ubic.basecode.io.reader.TestMapReader
-
- testReadBad() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
-
- testReadBlankCorner() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
-
- testReadChooseRows() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
-
- testReadChooseRowsBadfileName() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
-
- testReadChooseRowsSkipcols() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
-
- testReadInputStream() - Method in class ubic.basecode.io.reader.TestSparseRaggedDouble2DNamedMatrixReader
-
- testReadInputStreamColumnCount() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
-
- testReadInputStreamColumnCount() - Method in class ubic.basecode.io.reader.TestStringMatrixReader
-
- testReadInputStreamGotColName() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
-
- testReadInputStreamGotColName() - Method in class ubic.basecode.io.reader.TestStringMatrixReader
-
- testReadInputStreamGotColNameSkipColumn() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
-
- testReadInputStreamGotRowName() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
-
- testReadInputStreamGotRowName() - Method in class ubic.basecode.io.reader.TestStringMatrixReader
-
- testReadInputStreamMissing() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
-
- testReadInputStreamMissingBad() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
-
- testReadInputStreamMissingSpaces() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
-
- testReadInputStreamRowCount() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
-
- testReadInputStreamRowCount() - Method in class ubic.basecode.io.reader.TestStringMatrixReader
-
- testReadJW() - Method in class ubic.basecode.io.reader.TestSparseDoubleMatrixReader
-
- testReadNoHeader() - Method in class ubic.basecode.io.reader.TestMapReader
-
- testReadNoHeaderFile() - Method in class ubic.basecode.io.reader.TestMapReader
-
- testReadStream() - Method in class ubic.basecode.io.reader.TestSparseDoubleMatrixReader
-
- testReadStreamAdjList() - Method in class ubic.basecode.io.reader.TestSparseRaggedDouble2DNamedMatrixReader
-
- testReadStreamAdjListBig() - Method in class ubic.basecode.io.reader.TestSparseRaggedDouble2DNamedMatrixReader
-
- testReindexOnInitialize() - Method in class ubic.basecode.ontology.providers.AbstractOntologyServiceTest
-
- testRejectNonEnglish() - Method in class ubic.basecode.ontology.OntologyTermTest
-
- testRemoveMissing1() - Method in class ubic.basecode.dataStructure.matrix.MatrixUtilTest
-
- testRemoveMissing2() - Method in class ubic.basecode.dataStructure.matrix.MatrixUtilTest
-
- testRepeat() - Method in class ubic.basecode.math.RandomChooserTest
-
Check correctness of the sampling algorithm for choosing subsets of size 2.
- testRepeatSubset() - Method in class ubic.basecode.math.RandomChooserTest
-
Check correctness of the sampling algorithm for choosing subsets of size 2.
- testResourcetoPath() - Method in class ubic.basecode.util.FileToolsTest
-
- TestROC - Class in ubic.basecode.math
-
- TestROC() - Constructor for class ubic.basecode.math.TestROC
-
- TestRowAbsentFilter - Class in ubic.basecode.datafilter
-
See the file test/data/matrix-testing.xls for the validation.
- TestRowAbsentFilter() - Constructor for class ubic.basecode.datafilter.TestRowAbsentFilter
-
- TestRowAffyNameFilter - Class in ubic.basecode.datafilter
-
- TestRowAffyNameFilter() - Constructor for class ubic.basecode.datafilter.TestRowAffyNameFilter
-
- TestRowLevelFilter - Class in ubic.basecode.datafilter
-
- TestRowLevelFilter() - Constructor for class ubic.basecode.datafilter.TestRowLevelFilter
-
- TestRowMissingFilter - Class in ubic.basecode.datafilter
-
See the file test/data/matrix-testing.xls for the validation.
- TestRowMissingFilter() - Constructor for class ubic.basecode.datafilter.TestRowMissingFilter
-
- TestRowNameFilter - Class in ubic.basecode.datafilter
-
- TestRowNameFilter() - Constructor for class ubic.basecode.datafilter.TestRowNameFilter
-
- testRows() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testRows() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
-
- testRows() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
-
- testRows() - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrixTest
-
- testRows2() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testRunFixedE() - Method in class ubic.basecode.math.metaanalysis.TestMeanDifferenceMetaAnalysis
-
- testRunFixedQ() - Method in class ubic.basecode.math.metaanalysis.TestMeanDifferenceMetaAnalysis
-
- testRunFixedVar() - Method in class ubic.basecode.math.metaanalysis.TestMeanDifferenceMetaAnalysis
-
- testRunFixedZ() - Method in class ubic.basecode.math.metaanalysis.TestMeanDifferenceMetaAnalysis
-
- testRunRandomBSV() - Method in class ubic.basecode.math.metaanalysis.TestMeanDifferenceMetaAnalysis
-
- testRunRandomE() - Method in class ubic.basecode.math.metaanalysis.TestMeanDifferenceMetaAnalysis
-
- testRunRandomVar() - Method in class ubic.basecode.math.metaanalysis.TestMeanDifferenceMetaAnalysis
-
- testRunRandomZ() - Method in class ubic.basecode.math.metaanalysis.TestMeanDifferenceMetaAnalysis
-
- testRunUFEffect() - Method in class ubic.basecode.math.metaanalysis.TestCorrelationEffectMetaAnalysis
-
- testRunUFVar() - Method in class ubic.basecode.math.metaanalysis.TestCorrelationEffectMetaAnalysis
-
- testRunUFZscore() - Method in class ubic.basecode.math.metaanalysis.TestCorrelationEffectMetaAnalysis
-
- testRunURBSV() - Method in class ubic.basecode.math.metaanalysis.TestCorrelationEffectMetaAnalysis
-
- testRunZFEffect() - Method in class ubic.basecode.math.metaanalysis.TestCorrelationEffectMetaAnalysis
-
- testRunZFVar() - Method in class ubic.basecode.math.metaanalysis.TestCorrelationEffectMetaAnalysis
-
- testRunZFZscore() - Method in class ubic.basecode.math.metaanalysis.TestCorrelationEffectMetaAnalysis
-
- testRunZRBSV() - Method in class ubic.basecode.math.metaanalysis.TestCorrelationEffectMetaAnalysis
-
- testRunZRQval() - Method in class ubic.basecode.math.metaanalysis.TestCorrelationEffectMetaAnalysis
-
- testSampleKurtosis() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testSampleSkew() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testSampleStandardDeviation() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testSampleVariance() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testSaveImage() - Method in class ubic.basecode.graphics.MatrixDisplayTest
-
- testSaveImageStandardize() - Method in class ubic.basecode.graphics.MatrixDisplayTest
-
- testScaledDesign() - Method in class ubic.basecode.math.linalg.QRDecompositionTest
-
Case where the Design matrix values include values other than 1's and 0's.
- testSeen() - Method in class ubic.basecode.dataStructure.CountingMapTest
-
Test method for ca.elmonline.util.CountingMap#seen(java.lang.Object).
- testSeenValues() - Method in class ubic.basecode.dataStructure.StringToStringSetMapTest
-
- testSelectColumns() - Method in class ubic.basecode.dataStructure.matrix.MatrixUtilTest
-
- testSelectColumnsAndRows() - Method in class ubic.basecode.dataStructure.matrix.MatrixUtilTest
-
- testSelectColumnsAndRowsBad() - Method in class ubic.basecode.dataStructure.matrix.MatrixUtilTest
-
- testSelectRows() - Method in class ubic.basecode.dataStructure.matrix.MatrixUtilTest
-
- testSelfSquare() - Method in class ubic.basecode.math.TestMatrixStats
-
- testSet() - Method in class ubic.basecode.dataStructure.BitUtilTest
-
- testSet() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testSet() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
-
- testSet() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
-
Test method for ubic.basecode.dataStructure.matrix.SparseDoubleMatrix#set(int, int, double).
- testSet2() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
Test method for ubic.basecode.dataStructure.matrix.DenseDoubleMatrix#set(int, int, double).
- testSetByKeys() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
-
- testSetFormula() - Method in class ubic.basecode.io.excel.ExcelUtilTest
-
- testSetIntIntDouble() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testSetIntIntObject() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testSetObj() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
-
- testSingular() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
-
- testSingular2() - Method in class ubic.basecode.math.linalg.QRDecompositionTest
-
- testSingular2() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
-
Originally causes failures during summarization step.
- testSingularValueDecomposition() - Method in class ubic.basecode.math.SingularValueDecompositionTest
-
- testSize() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testSize() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
-
- testSize() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
-
- testSkew() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testSmallNumbers() - Method in class ubic.basecode.io.reader.TestDoubleMatrixReader
-
- testSortByColumnAbsoluteValue() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testSortedKeyList() - Method in class ubic.basecode.dataStructure.CountingMapTest
-
Test method for ca.elmonline.util.CountingMap#sortedEntrySet(java.lang.Object).
- testSortedKeyListBoolean() - Method in class ubic.basecode.dataStructure.CountingMapTest
-
Test method for ca.elmonline.util.CountingMap#sortedEntrySet(boolean).
- TestSparseDoubleMatrixReader - Class in ubic.basecode.io.reader
-
- TestSparseDoubleMatrixReader() - Constructor for class ubic.basecode.io.reader.TestSparseDoubleMatrixReader
-
- TestSparseRaggedDouble2DNamedMatrixReader - Class in ubic.basecode.io.reader
-
- TestSparseRaggedDouble2DNamedMatrixReader() - Constructor for class ubic.basecode.io.reader.TestSparseRaggedDouble2DNamedMatrixReader
-
- testSpearmanOneList1() - Method in class ubic.basecode.math.DistanceTest
-
- testSpearmanOneList2() - Method in class ubic.basecode.math.DistanceTest
-
- testSpearmanOneList3() - Method in class ubic.basecode.math.DistanceTest
-
- testSpearmanOneList4() - Method in class ubic.basecode.math.DistanceTest
-
- testSpearmanPvalueA() - Method in class ubic.basecode.math.CorrelationStatsTest
-
- testSpearmanPvalueA2() - Method in class ubic.basecode.math.CorrelationStatsTest
-
- testSpearmanPvalueB() - Method in class ubic.basecode.math.CorrelationStatsTest
-
- testSpearmanPvalueD() - Method in class ubic.basecode.math.CorrelationStatsTest
-
- testSpearmanPvalueD2() - Method in class ubic.basecode.math.CorrelationStatsTest
-
- testSpearmanPvalueE() - Method in class ubic.basecode.math.CorrelationStatsTest
-
- testSpearmanPvalueEh() - Method in class ubic.basecode.math.CorrelationStatsTest
-
- testSpearmanPvalueEm() - Method in class ubic.basecode.math.CorrelationStatsTest
-
- testSpearmanPvalueF() - Method in class ubic.basecode.math.CorrelationStatsTest
-
- testSpearmanPvalueG() - Method in class ubic.basecode.math.CorrelationStatsTest
-
- testSpearmanPvalueG2() - Method in class ubic.basecode.math.CorrelationStatsTest
-
- testSpearmanPvalueTDist() - Method in class ubic.basecode.math.CorrelationStatsTest
-
- testSpearmanRankCorrelation() - Method in class ubic.basecode.math.DistanceTest
-
- testSpearmanRankCorrelation2() - Method in class ubic.basecode.math.DistanceTest
-
- testSpearmanRankCorrelation3() - Method in class ubic.basecode.math.DistanceTest
-
- testSpearmanRankCorrelationNaN() - Method in class ubic.basecode.math.DistanceTest
-
- TestSpecFunc - Class in ubic.basecode.math
-
- TestSpecFunc() - Constructor for class ubic.basecode.math.TestSpecFunc
-
- testSqueezeVar() - Method in class ubic.basecode.math.linearmodels.ModeratedTstatTest
-
- testSqueezeVarB() - Method in class ubic.basecode.math.linearmodels.ModeratedTstatTest
-
Test based on GSE112792; see test-squeezevar.R
- testSqueezeVarWMissing() - Method in class ubic.basecode.math.linearmodels.ModeratedTstatTest
-
- testStandardDeviations() - Method in class ubic.basecode.math.TestMatrixRowStats
-
- testStandardize() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testStandardize() - Method in class ubic.basecode.math.TestMatrixStats
-
- TestStats - Class in ubic.basecode.math
-
- TestStats() - Constructor for class ubic.basecode.math.TestStats
-
- TestStringConverter - Class in ubic.basecode.io
-
$Id$
- TestStringConverter() - Constructor for class ubic.basecode.io.TestStringConverter
-
- teststringdata - Variable in class ubic.basecode.datafilter.AbstractTestFilter
-
- testStringFilter() - Method in class ubic.basecode.datafilter.TestRowAffyNameFilter
-
- testStringListEval() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
- testStringListEvalB() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
- TestStringMatrixReader - Class in ubic.basecode.io.reader
-
- TestStringMatrixReader() - Constructor for class ubic.basecode.io.reader.TestStringMatrixReader
-
- teststringmissingdata - Variable in class ubic.basecode.datafilter.AbstractTestFilter
-
- testStringToBytes() - Method in class ubic.basecode.io.TestByteArrayConverter
-
- testStringToDoubleArrayConversionSpeed() - Method in class ubic.basecode.io.TestByteArrayConverter
-
- TestStringUtil - Class in ubic.basecode.util
-
- TestStringUtil() - Constructor for class ubic.basecode.util.TestStringUtil
-
- testSubset() - Method in class ubic.basecode.dataStructure.matrix.StringMatrixTest
-
- testSubsetCols() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
-
- testSubsetColumns() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testSubsetColumns() - Method in class ubic.basecode.dataStructure.matrix.StringMatrixTest
-
- testSubsetRows() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testSubsetRows() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
-
- testSubsetRows() - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrixTest
-
- testSubsetRowsFail() - Method in class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrixTest
-
- testSum() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testSumArray() - Method in class ubic.basecode.math.TestMathUtil
-
- testSummation() - Method in class ubic.basecode.dataStructure.CountingMapTest
-
- testSumOfInversions() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testSumOfPowerDeviationsA() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testSumOfPowers() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testSumOfSquaredDeviations() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testSumOfSquares() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testSumOfSquaresDoubleMatrixNamed() - Method in class ubic.basecode.math.TestMatrixRowStats
-
- testSumOfSquaresDoubleMatrixNamedDoubleArrayList() - Method in class ubic.basecode.math.TestMatrixRowStats
-
- testSums() - Method in class ubic.basecode.math.TestMatrixRowStats
-
- testTestDir() - Method in class ubic.basecode.util.FileToolsTest
-
- testTestFileFile() - Method in class ubic.basecode.util.FileToolsTest
-
- testTestFileString() - Method in class ubic.basecode.util.FileToolsTest
-
- testThreeWaySingular() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
-
- testToArray() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testToArray() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
-
- testToBool() - Method in class ubic.basecode.dataStructure.BitUtilTest
-
- testToInteger() - Method in class ubic.basecode.dataStructure.matrix.IntegerMatrixTest
-
- testTopoSort() - Method in class ubic.basecode.dataStructure.graph.TestDirectedGraph
-
- testToString() - Method in class ubic.basecode.dataStructure.graph.TestDirectedGraph
-
- testToString() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testtostring() - Method in class ubic.basecode.dataStructure.matrix.DenseDouble3dMatrixTest
-
- testToString() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
-
- testToString() - Method in class ubic.basecode.dataStructure.matrix.StringMatrixTest
-
- testTotalBitCount() - Method in class ubic.basecode.dataStructure.matrix.CompressedNamedBitMatrixTest
-
- testTouch() - Method in class ubic.basecode.util.FileToolsTest
-
- testTreeView() - Method in class ubic.basecode.dataStructure.graph.TestDirectedGraph
-
- testTrigammaInverse() - Method in class ubic.basecode.math.TestSpecFunc
-
- testTrigammaInverseB() - Method in class ubic.basecode.math.TestSpecFunc
-
handling of missing and out of range values
- testTrimmedMean() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testTTest() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
- testTTestFail() - Method in class ubic.basecode.util.r.AbstractRClientTest
-
- testTwoStringHashKey() - Method in class ubic.basecode.util.TestStringUtil
-
- testTwoStringHashKeyB() - Method in class ubic.basecode.util.TestStringUtil
-
- testTwoWayAnovaUnfittable() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
-
Sanity check.
- testTwoWayAnovaWithInteractions() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
-
Check for problem reported by TF -- Gemma gives slightly different result.
- testTwoWayTwoLevelsOneContinousInteractionC() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
-
No missing values; Two-way ANOVA with interaction, PLUS a continuous covariate.
- testUnGzipFile() - Method in class ubic.basecode.util.FileToolsTest
-
- testUnzipFile() - Method in class ubic.basecode.util.FileToolsTest
-
- testVariance() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testVectorRegress() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
-
- testVectorWeightedRegress() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
-
- testVectorWeightedRegressWithMissing() - Method in class ubic.basecode.math.linearmodels.LeastSquaresFitTest
-
- testViewColumn() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testViewColumn() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
-
- testViewRow() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testViewRow() - Method in class ubic.basecode.dataStructure.matrix.SparseDoubleMatrixTest
-
- testViewRow2() - Method in class ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest
-
- testVoom() - Method in class ubic.basecode.math.linearmodels.MeanVarianceEstimatorTest
-
Test calculation of weights for LeastSquaresFitting.
- testWeightedHammingA() - Method in class ubic.basecode.math.StringDistanceTest
-
- testWeightedHammingB() - Method in class ubic.basecode.math.StringDistanceTest
-
- testWeightedHammingC() - Method in class ubic.basecode.math.StringDistanceTest
-
- testWeightedMean() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- testWeightedSuffixHammingA() - Method in class ubic.basecode.math.StringDistanceTest
-
- testWeightedSuffixHammingB() - Method in class ubic.basecode.math.StringDistanceTest
-
- testWeightedSuffixHammingC() - Method in class ubic.basecode.math.StringDistanceTest
-
- testWhereIs() - Method in class ubic.basecode.dataStructure.StringToStringSetMapTest
-
- TestWilcoxon - Class in ubic.basecode.math
-
Gold standard (?)
- TestWilcoxon() - Constructor for class ubic.basecode.math.TestWilcoxon
-
- testWilcoxonPExactA() - Method in class ubic.basecode.math.TestWilcoxon
-
- testWilxcoxonPExactB() - Method in class ubic.basecode.math.TestWilcoxon
-
- testWilxcoxonPExactC() - Method in class ubic.basecode.math.TestWilcoxon
-
- testWilxcoxonPExactD() - Method in class ubic.basecode.math.TestWilcoxon
-
- testWilxcoxonPGauss() - Method in class ubic.basecode.math.TestWilcoxon
-
- testWilxcoxonPGaussB() - Method in class ubic.basecode.math.TestWilcoxon
-
- testWilxcoxonPVolume() - Method in class ubic.basecode.math.TestWilcoxon
-
- testWilxcoxonPWithTies() - Method in class ubic.basecode.math.TestWilcoxon
-
- testWinsorizedMean() - Method in class ubic.basecode.math.TestDescriptiveWithMissing
-
- TestWishart - Class in ubic.basecode.math.distribution
-
- TestWishart() - Constructor for class ubic.basecode.math.distribution.TestWishart
-
- testWithNaNs() - Method in class ubic.basecode.math.TestRank
-
- testWithNaNs2() - Method in class ubic.basecode.math.TestRank
-
- testWithNaNs3() - Method in class ubic.basecode.math.TestRank
-
- testWrite3DMatrix() - Method in class ubic.basecode.io.writer.MatrixWriterTest
-
- testWriteMatrix() - Method in class ubic.basecode.io.writer.MatrixWriterTest
-
Test method for
ubic.basecode.io.writer.MatrixWriter#writeMatrix(ubic.basecode.dataStructure.matrix.NamedMatrix, boolean)
.
- testWriteMatrixB() - Method in class ubic.basecode.io.writer.MatrixWriterTest
-
- testWriteOutAsPNG() - Method in class ubic.basecode.graphics.MatrixDisplayTest
-
- testWriteOutAsPNG2() - Method in class ubic.basecode.graphics.MatrixDisplayTest
-
- testWriter() - Method in class ubic.basecode.io.writer.TestHistogramWriter
-
- testZDotProductDoubleMatrix1D() - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1DTest2
-
- testZDotProductDoubleMatrix1DHarder() - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1DTest2
-
- testZDotProductDoubleMatrix1DHarderReverse() - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1DTest2
-
- testZDotProductDoubleMatrix1DReverse() - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1DTest2
-
- testZSum() - Method in class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1DTest
-