Index (genetica-libraries 1.0.5 API)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

A - Static variable in class umcg.genetica.io.trityper.util.BaseAnnot
absSum(double[]) - Static method in class umcg.genetica.math.stats.Descriptives
acos(double) - Static method in class umcg.genetica.math.Fmath
acosh(double) - Static method in class umcg.genetica.math.Fmath
acot(double) - Static method in class umcg.genetica.math.Fmath
acot2(double, double) - Static method in class umcg.genetica.math.Fmath
acoth(double) - Static method in class umcg.genetica.math.Fmath
acovers(double) - Static method in class umcg.genetica.math.Fmath
acsc(double) - Static method in class umcg.genetica.math.Fmath
acsch(double) - Static method in class umcg.genetica.math.Fmath
addAnnotaion(E) - Method in class umcg.genetica.variantAnnotator.VariantAnnotator
addBoundary(String, Integer, int) - Method in class umcg.genetica.genomicboundaries.GenomicBoundaries: Method to add a Genomic Boundary to the Genmoic Boundaries set.
addBoundary(String, Integer, int, V) - Method in class umcg.genetica.genomicboundaries.GenomicBoundaries: Method to add a Genomic Boundary to the Genmoic Boundaries set.
addChrElements(String, List<E>) - Method in class umcg.genetica.collections.intervaltree.PerChrIntervalTree
addDataObject(UCSCDataObject) - Method in class umcg.genetica.io.ucsc.UCSCTrack
addDatasetToConcat(String) - Method in class umcg.genetica.io.trityper.util.TriTyperConcatDatasets
addExon(Exon) - Method in class umcg.genetica.containers.Transcript
addFilter(String, String) - Method in class umcg.genetica.io.gtf.GffAttributeFilter
addGene(Gene) - Method in class umcg.genetica.containers.Chromosome
addGene(int) - Method in class umcg.genetica.io.binInteraction.variant.BinaryInteractionVariantCreator
addPermutationDataset(String, String) - Method in class umcg.genetica.gwas.Independifier
addRegulomeDbFile(RegulomeDbFile) - Method in class umcg.genetica.io.regulomedb.RegulomeDbFiles
addTestedInteraction(String, String, String[]) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFileCreator
addTestedVariantGene(String, String) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFileCreator
addTopSNP(GWASSNP) - Method in class umcg.genetica.io.gwascatalog.GWASTrait
addTranscript(Transcript) - Method in class umcg.genetica.containers.Gene
addVariant(int) - Method in class umcg.genetica.io.binInteraction.gene.BinaryInteractionGeneCreator
aexsec(double) - Static method in class umcg.genetica.math.Fmath
ahav(double) - Static method in class umcg.genetica.math.Fmath
AndersonDarling - Class in umcg.genetica.math.stats: Anderson-Darling test for normality.
AndersonDarling.IS_DATA_NORMALIZED - Enum in umcg.genetica.math.stats
angle(double, double, double, double, double, double) - Static method in class umcg.genetica.math.Fmath
angle(double, double, double) - Static method in class umcg.genetica.math.Fmath
antilog(double) - Static method in class umcg.genetica.math.Fmath
antilog(float) - Static method in class umcg.genetica.math.Fmath
antilog10(double) - Static method in class umcg.genetica.math.Fmath
antilog10(float) - Static method in class umcg.genetica.math.Fmath
antilog2(double) - Static method in class umcg.genetica.math.Fmath
antilog2(float) - Static method in class umcg.genetica.math.Fmath
append(char) - Method in class umcg.genetica.io.text.TextFile
append(CharSequence) - Method in class umcg.genetica.io.text.TextFile
appendMappedGenes(HashSet<String>) - Method in class umcg.genetica.io.gwascatalog.GWASTrait
appendPrefixToColnames(DoubleMatrixDataset<String, String>, String) - Static method in class umcg.genetica.math.matrix2.MatrixHandling: Append a static prefix to the column names
appendReportedGenes(HashSet<String>) - Method in class umcg.genetica.io.gwascatalog.GWASTrait
appendStringToColnames(DoubleMatrixDataset<String, String>, String) - Static method in class umcg.genetica.math.matrix.MatrixHandling
areAllCovariatesTestedForAllVariantGenes() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
arrayAbs(double[]) - Static method in class umcg.genetica.math.Fmath
arrayAbs(float[]) - Static method in class umcg.genetica.math.Fmath
arrayAbs(long[]) - Static method in class umcg.genetica.math.Fmath
arrayAbs(int[]) - Static method in class umcg.genetica.math.Fmath
arrayMultByConstant(double[], double) - Static method in class umcg.genetica.math.Fmath
arrayMultByConstant(int[], double) - Static method in class umcg.genetica.math.Fmath
arrayMultByConstant(double[], int) - Static method in class umcg.genetica.math.Fmath
arrayMultByConstant(int[], int) - Static method in class umcg.genetica.math.Fmath
arrayPositiveElementsSum(long[]) - Static method in class umcg.genetica.math.Fmath
arrayProduct(double[]) - Static method in class umcg.genetica.math.Fmath
arrayProduct(float[]) - Static method in class umcg.genetica.math.Fmath
arrayProduct(int[]) - Static method in class umcg.genetica.math.Fmath
arrayProduct(long[]) - Static method in class umcg.genetica.math.Fmath
arraySum(double[]) - Static method in class umcg.genetica.math.Fmath
arraySum(float[]) - Static method in class umcg.genetica.math.Fmath
arraySum(int[]) - Static method in class umcg.genetica.math.Fmath
arraySum(long[]) - Static method in class umcg.genetica.math.Fmath
asec(double) - Static method in class umcg.genetica.math.Fmath
asech(double) - Static method in class umcg.genetica.math.Fmath
ASESSEDALLELE - Static variable in class umcg.genetica.io.trityper.QTLTextFile
asin(double) - Static method in class umcg.genetica.math.Fmath
asinh(double) - Static method in class umcg.genetica.math.Fmath
associateAnovaScoreAndItemOfInterest(DoubleMatrixDataset<String, String>, HashMap<String, HashMap<String, String>>) - Static method in class umcg.genetica.methylation.AssociatingPcasWithAnnotation: Test for difference between all GSE groups with Anova.
associateScoreAndItemOfInterest(DoubleMatrixDataset<String, String>, HashMap<String, HashMap<String, String>>, ArrayList<String>) - Static method in class umcg.genetica.methylation.AssociatingPcasWithAnnotation: Test for difference between 2 groups with T-test.
AssociatingPcasWithAnnotation - Class in umcg.genetica.methylation
AssociatingPcasWithAnnotation() - Constructor for class umcg.genetica.methylation.AssociatingPcasWithAnnotation
atan(double) - Static method in class umcg.genetica.math.Fmath
atan2(double, double) - Static method in class umcg.genetica.math.Fmath
atanh(double) - Static method in class umcg.genetica.math.Fmath
AUC - Class in umcg.genetica.math.stats
AUC() - Constructor for class umcg.genetica.math.stats.AUC
available() - Method in class com.mastfrog.util.streams.HashingInputStream
averageIdenticalAbscissae() - Static method in class umcg.genetica.math.interpolation.CubicSpline
avers(double) - Static method in class umcg.genetica.math.Fmath

B

backwardslash - Static variable in class umcg.genetica.text.Strings
BaseAnnot - Class in umcg.genetica.io.trityper.util
BaseAnnot() - Constructor for class umcg.genetica.io.trityper.util.BaseAnnot
BeagleImputedToTriTyper - Class in umcg.genetica.io.trityper.converters
BeagleImputedToTriTyper() - Constructor for class umcg.genetica.io.trityper.converters.BeagleImputedToTriTyper
BedEntry - Class in umcg.genetica.io.bed
BedEntry(String, int, int) - Constructor for class umcg.genetica.io.bed.BedEntry
BedEntry(String, int, int, String, double) - Constructor for class umcg.genetica.io.bed.BedEntry
BedFile - Class in umcg.genetica.io.bed
BedFile(String) - Constructor for class umcg.genetica.io.bed.BedFile
BedFile(String, boolean, boolean) - Constructor for class umcg.genetica.io.bed.BedFile
BedFile(File) - Constructor for class umcg.genetica.io.bed.BedFile
BedFile(File, boolean, boolean) - Constructor for class umcg.genetica.io.bed.BedFile
BedGraphEntry - Class in umcg.genetica.io.bedgraph
BedGraphEntry(String, int, int, double) - Constructor for class umcg.genetica.io.bedgraph.BedGraphEntry
BedGraphFile - Class in umcg.genetica.io.bedgraph
BedGraphFile(String) - Constructor for class umcg.genetica.io.bedgraph.BedGraphFile
BedGraphFile(String, boolean, boolean) - Constructor for class umcg.genetica.io.bedgraph.BedGraphFile
BedGraphFile(File) - Constructor for class umcg.genetica.io.bedgraph.BedGraphFile
BedGraphFile(File, boolean, boolean) - Constructor for class umcg.genetica.io.bedgraph.BedGraphFile
benchmark(String, int) - Static method in class umcg.genetica.io.bin.RandomAccessFile: Benchmark the performance of the new RandomAccessFile class.
Beta(DoubleMatrixDataset<String, String>, DoubleMatrixDataset<String, String>) - Static method in class umcg.genetica.methylation.ConverteUandMTo
betaToZ(double, double, double) - Static method in class umcg.genetica.math.stats.ZScores
BinaryFile - Class in umcg.genetica.io.bin
BinaryFile(String, boolean) - Constructor for class umcg.genetica.io.bin.BinaryFile
BinaryFile(String, boolean, int) - Constructor for class umcg.genetica.io.bin.BinaryFile
BinaryGZipFloatMatrix - Class in umcg.genetica.io.trityper.bin
BinaryGZipFloatMatrix(String, boolean) - Constructor for class umcg.genetica.io.trityper.bin.BinaryGZipFloatMatrix
BinaryInteractionCohort - Class in umcg.genetica.io.binInteraction
BinaryInteractionCohort(String, int) - Constructor for class umcg.genetica.io.binInteraction.BinaryInteractionCohort
BinaryInteractionCovariateIterator - Class in umcg.genetica.io.binInteraction
BinaryInteractionCovariateIterator(String, String, int[], BinaryInteractionFile, long, BinaryInteractionQtlZscores) - Constructor for class umcg.genetica.io.binInteraction.BinaryInteractionCovariateIterator
BinaryInteractionFile - Class in umcg.genetica.io.binInteraction
BinaryInteractionFile(File, boolean, BinaryInteractionCohort[], BinaryInteractionGene[], BinaryInteractionVariant[], String[], int[][], long, boolean, boolean, boolean, boolean, String, long, long, long) - Constructor for class umcg.genetica.io.binInteraction.BinaryInteractionFile
BinaryInteractionFileConstructorBuilder - Class in umcg.genetica.io.binInteraction
BinaryInteractionFileConstructorBuilder() - Constructor for class umcg.genetica.io.binInteraction.BinaryInteractionFileConstructorBuilder
BinaryInteractionFileCreator - Class in umcg.genetica.io.binInteraction
BinaryInteractionFileCreator(File, BinaryInteractionVariantCreator[], BinaryInteractionGeneCreator[], BinaryInteractionCohort[], String[], boolean, boolean, boolean, boolean) - Constructor for class umcg.genetica.io.binInteraction.BinaryInteractionFileCreator
BinaryInteractionFileException - Exception in umcg.genetica.io.binInteraction
BinaryInteractionFileException() - Constructor for exception umcg.genetica.io.binInteraction.BinaryInteractionFileException
BinaryInteractionFileException(String) - Constructor for exception umcg.genetica.io.binInteraction.BinaryInteractionFileException
BinaryInteractionFileException(String, Throwable) - Constructor for exception umcg.genetica.io.binInteraction.BinaryInteractionFileException
BinaryInteractionFileException(Throwable) - Constructor for exception umcg.genetica.io.binInteraction.BinaryInteractionFileException
BinaryInteractionGene - Interface in umcg.genetica.io.binInteraction.gene
BinaryInteractionGeneAbstract - Class in umcg.genetica.io.binInteraction.gene
BinaryInteractionGeneAbstract(String, String, int, int) - Constructor for class umcg.genetica.io.binInteraction.gene.BinaryInteractionGeneAbstract
BinaryInteractionGeneCreator - Class in umcg.genetica.io.binInteraction.gene
BinaryInteractionGeneCreator(String, String, int, int) - Constructor for class umcg.genetica.io.binInteraction.gene.BinaryInteractionGeneCreator
BinaryInteractionGeneCreator(String) - Constructor for class umcg.genetica.io.binInteraction.gene.BinaryInteractionGeneCreator
BinaryInteractionGeneStatic - Class in umcg.genetica.io.binInteraction.gene
BinaryInteractionGeneStatic(String, String, int, int, int[]) - Constructor for class umcg.genetica.io.binInteraction.gene.BinaryInteractionGeneStatic
BinaryInteractionQtlZscores - Class in umcg.genetica.io.binInteraction
BinaryInteractionQtlZscores(double[], int[], double) - Constructor for class umcg.genetica.io.binInteraction.BinaryInteractionQtlZscores
BinaryInteractionQtlZscores(double[], int[]) - Constructor for class umcg.genetica.io.binInteraction.BinaryInteractionQtlZscores
BinaryInteractionQtlZscores(double, int) - Constructor for class umcg.genetica.io.binInteraction.BinaryInteractionQtlZscores
BinaryInteractionQtlZscores(double) - Constructor for class umcg.genetica.io.binInteraction.BinaryInteractionQtlZscores
BinaryInteractionQueryResult - Class in umcg.genetica.io.binInteraction
BinaryInteractionQueryResult(String, String, String, BinaryInteractionQtlZscores, BinaryInteractionZscores) - Constructor for class umcg.genetica.io.binInteraction.BinaryInteractionQueryResult
BinaryInteractionVariant - Interface in umcg.genetica.io.binInteraction.variant
BinaryInteractionVariantAbstract - Class in umcg.genetica.io.binInteraction.variant
BinaryInteractionVariantAbstract(String, String, int, Allele, Allele) - Constructor for class umcg.genetica.io.binInteraction.variant.BinaryInteractionVariantAbstract
BinaryInteractionVariantCreator - Class in umcg.genetica.io.binInteraction.variant
BinaryInteractionVariantCreator(String, String, int, Allele, Allele) - Constructor for class umcg.genetica.io.binInteraction.variant.BinaryInteractionVariantCreator
BinaryInteractionVariantStatic - Class in umcg.genetica.io.binInteraction.variant
BinaryInteractionVariantStatic(String, String, int, Allele, Allele, int[]) - Constructor for class umcg.genetica.io.binInteraction.variant.BinaryInteractionVariantStatic
BinaryInteractionZscores - Class in umcg.genetica.io.binInteraction
BinaryInteractionZscores(int[], double[], double[], double[], double[], double[], double, double, double, double) - Constructor for class umcg.genetica.io.binInteraction.BinaryInteractionZscores
BinaryInteractionZscores(int[], double[], double[], double[], double[], double[]) - Constructor for class umcg.genetica.io.binInteraction.BinaryInteractionZscores
BinaryInteractionZscores(int[], double[], double[], double[], double[]) - Constructor for class umcg.genetica.io.binInteraction.BinaryInteractionZscores
BinaryInteractionZscores(int, double, double, double, double, double) - Constructor for class umcg.genetica.io.binInteraction.BinaryInteractionZscores
BinaryInteractionZscores(int[], double[], double[], double[], double[], double, double, double) - Constructor for class umcg.genetica.io.binInteraction.BinaryInteractionZscores
BinaryInteractionZscores(double, double, double, double) - Constructor for class umcg.genetica.io.binInteraction.BinaryInteractionZscores
BinaryInteractionZscores(double, double, double) - Constructor for class umcg.genetica.io.binInteraction.BinaryInteractionZscores
BinaryResultDataset - Class in umcg.genetica.io.trityper.bin
BinaryResultDataset(String, String, int) - Constructor for class umcg.genetica.io.trityper.bin.BinaryResultDataset
BinaryResultProbe - Class in umcg.genetica.io.trityper.bin
BinaryResultProbe() - Constructor for class umcg.genetica.io.trityper.bin.BinaryResultProbe
BinaryResultProbeSummary - Class in umcg.genetica.io.trityper.bin
BinaryResultProbeSummary(String, boolean) - Constructor for class umcg.genetica.io.trityper.bin.BinaryResultProbeSummary
BinaryResultSNP - Class in umcg.genetica.io.trityper.bin
BinaryResultSNP() - Constructor for class umcg.genetica.io.trityper.bin.BinaryResultSNP
BinaryResultSNPSummary - Class in umcg.genetica.io.trityper.bin
BinaryResultSNPSummary(String, boolean) - Constructor for class umcg.genetica.io.trityper.bin.BinaryResultSNPSummary
Binning - Class in umcg.genetica.math.stats
Binning() - Constructor for class umcg.genetica.math.stats.Binning
buffer - Variable in class umcg.genetica.io.bin.RandomAccessFile: The buffer used to load the data.
BufferedSNPLoader - Class in umcg.genetica.io.trityper
BufferedSNPLoader(RandomAccessFile, Boolean[], Boolean[]) - Constructor for class umcg.genetica.io.trityper.BufferedSNPLoader
BufferedSNPLoader(RandomAccessFile, RandomAccessFile, Boolean[], Boolean[]) - Constructor for class umcg.genetica.io.trityper.BufferedSNPLoader
bufferStart - Variable in class umcg.genetica.io.bin.RandomAccessFile: The offset in bytes of the start of the buffer, from the start of the file.
byteTOdouble(byte[]) - Static method in class umcg.genetica.math.Fmath
byteTOfloat(byte[]) - Static method in class umcg.genetica.math.Fmath
byteTOint(byte[]) - Static method in class umcg.genetica.math.Fmath
byteTOlong(byte[]) - Static method in class umcg.genetica.math.Fmath
byteTOshort(byte[]) - Static method in class umcg.genetica.math.Fmath

C

C - Static variable in class umcg.genetica.io.trityper.util.BaseAnnot
C_LIGHT - Static variable in class umcg.genetica.math.Fmath
calcAndSubtractMean() - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
calcBMIimperial(double, double) - Static method in class umcg.genetica.math.Fmath
calcBMImetric(double, double) - Static method in class umcg.genetica.math.Fmath
calcDeriv() - Method in class umcg.genetica.math.interpolation.CubicSpline
calcMeanAndVariance() - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
calcPosOnCircle(double, double, double, double) - Static method in class umcg.genetica.math.Goniometry
calculateExactHWEPValue(int, int, int) - Static method in class umcg.genetica.math.stats.HWE
calculateFisherTwoTail() - Method in class umcg.genetica.math.stats.FisherExactTest
calculateProbeCoexpression(String) - Method in class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
calculateSizeInteractionResultBlock(int, boolean, boolean) - Static method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
calculateSizeNormalQtlBlock(int, boolean) - Static method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
calcWeightFromBMIimperial(double, double) - Static method in class umcg.genetica.math.Fmath
calcWeightFromBMImetric(double, double) - Static method in class umcg.genetica.math.Fmath
call() - Method in class umcg.genetica.io.concurrent.DoubleParseTask
call() - Method in class umcg.genetica.math.stats.concurrent.ConcurrentCorrelationTask
call() - Method in class umcg.genetica.math.stats.concurrent.ConcurrentCovariationTask
calorieToJoule(double) - Static method in class umcg.genetica.math.Fmath
canExecute(String) - Static method in class umcg.genetica.io.Gpio
canRead(String) - Static method in class umcg.genetica.io.Gpio
canWrite(String) - Static method in class umcg.genetica.io.Gpio
celsiusToFahren(double) - Static method in class umcg.genetica.math.Fmath
celsiusToKelvin(double) - Static method in class umcg.genetica.math.Fmath
centerAndScaleColum(DoubleMatrix2D) - Static method in class umcg.genetica.math.matrix2.MatrixTools
centerColum(DoubleMatrix2D) - Static method in class umcg.genetica.math.matrix2.MatrixTools
CheckAssocationMultipleGeneProbes - Class in umcg.genetica.util
CheckAssocationMultipleGeneProbes() - Constructor for class umcg.genetica.util.CheckAssocationMultipleGeneProbes
checkBetaValues(DoubleMatrixDataset<String, String>, boolean) - Static method in class umcg.genetica.methylation.CheckMatrixForValidBetaValues: Check if all probe values are actually between 0 and 1.
checkForIdenticalPoints() - Method in class umcg.genetica.math.interpolation.CubicSpline
CheckMatrixForValidBetaValues - Class in umcg.genetica.methylation
CheckMatrixForValidBetaValues() - Constructor for class umcg.genetica.methylation.CheckMatrixForValidBetaValues
checkMerge(String[], String) - Method in class umcg.genetica.io.trityper.util.TriTyperGenotypeDataMerger
checkMinAndMaxPerSample(DoubleMatrixDataset<String, String>, boolean) - Static method in class umcg.genetica.methylation.CheckMatrixForValidBetaValues: Check if all probe values are actually between 0 and 1.
checkPrecision(double) - Static method in class umcg.genetica.math.Fmath
checkPrecision(float) - Static method in class umcg.genetica.math.Fmath
ChiSquare - Class in umcg.genetica.math.stats
ChiSquare() - Constructor for class umcg.genetica.math.stats.ChiSquare
chr - Variable in class umcg.genetica.containers.SortableSNP
ChrAnnotation - Class in umcg.genetica.io.trityper.util
ChrAnnotation() - Constructor for class umcg.genetica.io.trityper.util.ChrAnnotation
chrIterator(String) - Method in class umcg.genetica.collections.ChrPosMap
chrIterator(String) - Method in class umcg.genetica.collections.ChrPosTreeMap
Chromosome - Class in umcg.genetica.containers
Chromosome(String) - Constructor for class umcg.genetica.containers.Chromosome
chrpos - Variable in class umcg.genetica.containers.SortableSNP
ChrPosMap<E> - Class in umcg.genetica.collections
ChrPosMap() - Constructor for class umcg.genetica.collections.ChrPosMap
ChrPosTreeMap<E> - Class in umcg.genetica.collections
ChrPosTreeMap() - Constructor for class umcg.genetica.collections.ChrPosTreeMap
chrToSNP - Variable in class umcg.genetica.ncbi.dbsnp.SNPAnnotation
chrToUniquePositions - Variable in class umcg.genetica.ncbi.dbsnp.SNPAnnotation
cisAnalysis - Variable in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDatasetSettings
CISTRANS - Static variable in class umcg.genetica.io.trityper.QTLTextFile
clearData() - Method in class umcg.genetica.io.trityper.EQTL
clearGenotypes() - Method in class umcg.genetica.io.trityper.SNP
clearMetaData() - Method in class umcg.genetica.io.trityper.bin.BinaryResultProbe
clearMetaData() - Method in class umcg.genetica.io.trityper.bin.BinaryResultSNP
clearProbeObjects() - Method in class umcg.genetica.io.trityper.bin.BinaryResultDataset
close() - Method in class com.mastfrog.util.streams.HashingInputStream
close() - Method in class com.mastfrog.util.streams.HashingOutputStream
close() - Method in class umcg.genetica.console.ProgressBar
close() - Method in class umcg.genetica.io.bin.BinaryFile
close() - Method in class umcg.genetica.io.bin.RandomAccessFile: Close the file, and release any associated system resources.
close() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
close() - Method in interface umcg.genetica.io.gtf.GffReaderInterface
close() - Method in class umcg.genetica.io.gtf.GtfReader
close() - Method in class umcg.genetica.io.text.TextFile
close() - Method in class umcg.genetica.io.trityper.bin.BinaryGZipFloatMatrix
close() - Method in class umcg.genetica.io.trityper.bin.BinaryResultDataset
close() - Method in class umcg.genetica.io.trityper.bin.BinaryResultProbeSummary
close() - Method in class umcg.genetica.io.trityper.bin.BinaryResultSNPSummary
close() - Method in class umcg.genetica.io.trityper.BufferedSNPLoader
close() - Method in class umcg.genetica.io.trityper.SNPLoader
close() - Method in class umcg.genetica.io.trityper.WGAFileMatrixGenotype
close() - Method in class umcg.genetica.io.trityper.WGAFileMatrixImputedDosage
close() - Method in class umcg.genetica.io.trityper.WGAFileMatrixRawData
closeMatrix() - Method in class umcg.genetica.io.trityper.bin.BinaryResultDataset
colObjects - Variable in class umcg.genetica.math.matrix.DoubleMatrixDatasetAC: Deprecated.
colon - Static variable in class umcg.genetica.io.text.TextFile
colon - Static variable in class umcg.genetica.text.Strings
colsToInclude - Variable in class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
colsToInclude - Variable in class umcg.genetica.math.matrix.DoubleMatrixDatasetRA: Deprecated.
columns() - Method in class umcg.genetica.math.matrix2.DoubleMatrixDataset
com.mastfrog.util.streams - package com.mastfrog.util.streams
combineBasedOnCols(ArrayList<DoubleMatrixDataset>) - Static method in class umcg.genetica.math.matrix.MergeDoubleMatrices: Merge a set of matrices based on column identifiers.
combineBasedOnCols(ArrayList<DoubleMatrixDataset<String, String>>) - Static method in class umcg.genetica.math.matrix2.MergeDoubleMatrices: Merge a set of matrices based on column identifiers.
combineBasedOnRows(ArrayList<DoubleMatrixDataset>) - Static method in class umcg.genetica.math.matrix.MergeDoubleMatrices: Merge a set of matrices based on row identifiers.
combineBasedOnRows(ArrayList<DoubleMatrixDataset<String, String>>) - Static method in class umcg.genetica.math.matrix2.MergeDoubleMatrices: Merge a set of matrices based on row identifiers.
combinePrioritizerDatasetsMergeCommonSNPs(String, String, String, String) - Method in class umcg.genetica.io.trityper.util.TriTyperGenotypeDataMerger
comma - Static variable in class umcg.genetica.io.text.TextFile
comma - Static variable in class umcg.genetica.text.Strings
comp - Variable in class umcg.genetica.util.RankArray
comp - Variable in class umcg.genetica.util.RankDoubleArray
comp - Variable in class umcg.genetica.util.RankIntArray
compare(Range, Range) - Method in class umcg.genetica.collections.intervaltree.RangeEndReverseComparator
compare(Range, Range) - Method in class umcg.genetica.collections.intervaltree.RangeStartComparator
compare(EQTL) - Method in class umcg.genetica.io.trityper.EQTL
compare(SNP[]) - Static method in class umcg.genetica.io.trityper.util.CompareAllelicDirections
compare(double, double) - Static method in class umcg.genetica.math.Fmath
compare(int, int) - Static method in class umcg.genetica.math.Fmath
compare(long, long) - Static method in class umcg.genetica.math.Fmath
compare(float, float) - Static method in class umcg.genetica.math.Fmath
compare(byte, byte) - Static method in class umcg.genetica.math.Fmath
compare(short, short) - Static method in class umcg.genetica.math.Fmath
compare(double[], double[]) - Static method in class umcg.genetica.math.Fmath
compare(float[], float[]) - Static method in class umcg.genetica.math.Fmath
compare(int[], int[]) - Static method in class umcg.genetica.math.Fmath
compare(long[], long[]) - Static method in class umcg.genetica.math.Fmath
CompareAllelicDirections - Class in umcg.genetica.io.trityper.util
CompareAllelicDirections() - Constructor for class umcg.genetica.io.trityper.util.CompareAllelicDirections
compareTo(Pair<L, R>) - Method in class umcg.genetica.containers.Pair
compareTo(SortableSNP) - Method in class umcg.genetica.containers.SortableSNP
compareTo(GenomicBoundary) - Method in class umcg.genetica.genomicboundaries.GenomicBoundary
compareTo(EQTL) - Method in class umcg.genetica.io.trityper.EQTL
compareTo(TriTyperGeneticalGenomicsDataset) - Method in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDataset
compareTo(UCSCDataObject) - Method in class umcg.genetica.io.ucsc.UCSCDataObject
compareTo(UCSCTrack) - Method in class umcg.genetica.io.ucsc.UCSCTrack
compareToVerbose(EQTL) - Method in class umcg.genetica.io.trityper.EQTL
compdouble - Variable in class umcg.genetica.util.RankArray
concat(String[], Pattern) - Static method in class umcg.genetica.text.Strings
concat(Object[], Pattern) - Static method in class umcg.genetica.text.Strings
concat(double[], Pattern) - Static method in class umcg.genetica.text.Strings
concat(double[], DecimalFormat, Pattern) - Static method in class umcg.genetica.text.Strings
concat(float[], DecimalFormat, Pattern) - Static method in class umcg.genetica.text.Strings
concat(int[], Pattern) - Static method in class umcg.genetica.text.Strings
concat(List<String>, Pattern) - Static method in class umcg.genetica.text.Strings
concat(String[], Pattern, int, int) - Static method in class umcg.genetica.text.Strings
concatenate(double[], double[]) - Static method in class umcg.genetica.math.Fmath
concatenate(float[], float[]) - Static method in class umcg.genetica.math.Fmath
concatenate(int[], int[]) - Static method in class umcg.genetica.math.Fmath
concatenate(long[], long[]) - Static method in class umcg.genetica.math.Fmath
concatenate(short[], short[]) - Static method in class umcg.genetica.math.Fmath
concatenate(byte[], byte[]) - Static method in class umcg.genetica.math.Fmath
concatenate(char[], char[]) - Static method in class umcg.genetica.math.Fmath
concatenate(String[], String[]) - Static method in class umcg.genetica.math.Fmath
concatenate(Object[], Object[]) - Static method in class umcg.genetica.math.Fmath
ConcurrentCorrelation - Class in umcg.genetica.math.stats.concurrent
ConcurrentCorrelation() - Constructor for class umcg.genetica.math.stats.concurrent.ConcurrentCorrelation
ConcurrentCorrelation(int) - Constructor for class umcg.genetica.math.stats.concurrent.ConcurrentCorrelation
ConcurrentCorrelationTask - Class in umcg.genetica.math.stats.concurrent
ConcurrentCorrelationTask(double[][], double[], int) - Constructor for class umcg.genetica.math.stats.concurrent.ConcurrentCorrelationTask
ConcurrentCovariation - Class in umcg.genetica.math.stats.concurrent
ConcurrentCovariation() - Constructor for class umcg.genetica.math.stats.concurrent.ConcurrentCovariation
ConcurrentCovariation(int) - Constructor for class umcg.genetica.math.stats.concurrent.ConcurrentCovariation
ConcurrentCovariationTask - Class in umcg.genetica.math.stats.concurrent
ConcurrentCovariationTask(double[][], double[], int) - Constructor for class umcg.genetica.math.stats.concurrent.ConcurrentCovariationTask
confineProbesToProbesMappingToAnyChromosome - Variable in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDatasetSettings
confineProbesToProbesThatMapToChromosome - Variable in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDatasetSettings
confineToProbes(THashSet<String>) - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
ConsoleGUIElems - Class in umcg.genetica.console
ConsoleGUIElems() - Constructor for class umcg.genetica.console.ConsoleGUIElems
containsCovariant(String) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
containsGene(String) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
containsInteraction(String, String, String) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
containsNaNs(double[][]) - Static method in class umcg.genetica.math.matrix.MatrixTools
containsNaNs(DoubleMatrix2D) - Static method in class umcg.genetica.math.matrix2.MatrixTools
containsVariant(String) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
containsVariantGene(String, String) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
containsZeros(double[][]) - Static method in class umcg.genetica.math.matrix.MatrixTools
containsZeros(DoubleMatrix2D) - Static method in class umcg.genetica.math.matrix2.MatrixTools
convert(String, String) - Method in class umcg.genetica.io.trityper.converters.InversionCallsToTriTyper
convert(String, String, String) - Static method in class umcg.genetica.io.trityper.converters.TriTyperToMachImputedTransposed
convert(String, String, String) - Method in class umcg.genetica.io.trityper.converters.TriTyperToTabSeparated
convert(String, String, String) - Method in class umcg.genetica.io.trityper.converters.TriTyperToVCF
ConvertBetaAndMvalues - Class in umcg.genetica.methylation
ConvertBetaAndMvalues() - Constructor for class umcg.genetica.methylation.ConvertBetaAndMvalues
convertCorrelationToZScore(int, double) - Static method in class umcg.genetica.math.stats.Correlation
ConvertDoubleMatrixDataToTriTyper - Class in umcg.genetica.io.trityper
ConvertDoubleMatrixDataToTriTyper() - Constructor for class umcg.genetica.io.trityper.ConvertDoubleMatrixDataToTriTyper
ConverteUandMTo - Class in umcg.genetica.methylation
ConverteUandMTo() - Constructor for class umcg.genetica.methylation.ConverteUandMTo
convertGMTFileToPlainTextBinaryNetwork(String, String, boolean, boolean) - Static method in class umcg.genetica.io.text.converters.NetworkConverter
convertMinimacImputedToTriTyper(String, String) - Static method in class umcg.genetica.io.trityper.converters.MinimacImputedToTriTyper
convertPileupToVcf(PileupFile, String, File, RandomAccessGenotypeData, int) - Static method in class umcg.genetica.io.pileup.PileupToVcf: Parse pileup file and create vcf files with only SNPs that are in referenceGenotype data.
convertPileupToVcf2(PileupFile, String, File, RandomAccessGenotypeData, int) - Static method in class umcg.genetica.io.pileup.PileupToVcf: Parse pileup file and create vcf files with only SNPs that are in referenceGenotype data.
convertPlainTextDoubleMatrixToPlainTextEdgeList(String, String, String, String) - Static method in class umcg.genetica.io.text.converters.NetworkConverter
convertSingleFileMinimacImputedToTriTyper(String, String) - Static method in class umcg.genetica.io.trityper.converters.MinimacImputedToTriTyper
convertToComplementaryAlleles(byte[]) - Static method in class umcg.genetica.io.trityper.util.BaseAnnot
convertZscoreToPvalue(double) - Static method in class umcg.genetica.math.stats.Descriptives
copy(double[]) - Static method in class umcg.genetica.math.Fmath
copy(float[]) - Static method in class umcg.genetica.math.Fmath
copy(int[]) - Static method in class umcg.genetica.math.Fmath
copy(long[]) - Static method in class umcg.genetica.math.Fmath
copy(double[][]) - Static method in class umcg.genetica.math.Fmath
copy(float[][]) - Static method in class umcg.genetica.math.Fmath
copy(int[][]) - Static method in class umcg.genetica.math.Fmath
copy(long[][]) - Static method in class umcg.genetica.math.Fmath
copy(double[][][]) - Static method in class umcg.genetica.math.Fmath
copy(float[][][]) - Static method in class umcg.genetica.math.Fmath
copy(int[][][]) - Static method in class umcg.genetica.math.Fmath
copy(long[][][]) - Static method in class umcg.genetica.math.Fmath
copy(double[][][][]) - Static method in class umcg.genetica.math.Fmath
copy(float[][][][]) - Static method in class umcg.genetica.math.Fmath
copy(int[][][][]) - Static method in class umcg.genetica.math.Fmath
copy(long[][][][]) - Static method in class umcg.genetica.math.Fmath
copy(String[]) - Static method in class umcg.genetica.math.Fmath
copy(String[][]) - Static method in class umcg.genetica.math.Fmath
copy(String[][][]) - Static method in class umcg.genetica.math.Fmath
copy(String[][][][]) - Static method in class umcg.genetica.math.Fmath
copy(boolean[]) - Static method in class umcg.genetica.math.Fmath
copy(boolean[][]) - Static method in class umcg.genetica.math.Fmath
copy(boolean[][][]) - Static method in class umcg.genetica.math.Fmath
copy(boolean[][][][]) - Static method in class umcg.genetica.math.Fmath
copy(char[]) - Static method in class umcg.genetica.math.Fmath
copy(char[][]) - Static method in class umcg.genetica.math.Fmath
copy(char[][][]) - Static method in class umcg.genetica.math.Fmath
copy(char[][][][]) - Static method in class umcg.genetica.math.Fmath
copy(Object) - Static method in class umcg.genetica.math.Fmath
CopyDoubleArrayArray(double[][]) - Static method in class umcg.genetica.methylation.DeepCopy
copyFile(File, File) - Static method in class umcg.genetica.io.Gpio
copyFile(String, String) - Static method in class umcg.genetica.io.Gpio
copyObject(Object) - Static method in class umcg.genetica.math.Fmath
correlate(double[], double[]) - Static method in class umcg.genetica.math.stats.Correlation: Fast correlation of two double[]
correlate(double, double, double[], double[]) - Static method in class umcg.genetica.math.stats.Correlation: Fast correlation of two double[] with their mean values
correlate(double[], double[], double, double, double, double) - Static method in class umcg.genetica.math.stats.Correlation
correlateMeanCenteredData(double[], double[], double, double) - Static method in class umcg.genetica.math.stats.Correlation
correlateMeanCenteredData(double[], double[], double) - Static method in class umcg.genetica.math.stats.Correlation
correlateScoreAndItemOfInterest(DoubleMatrixDataset<String, String>, HashMap<String, HashMap<String, String>>, String, boolean) - Static method in class umcg.genetica.methylation.AssociatingPcasWithAnnotation: Correlate values of interest to age
Correlation - Class in umcg.genetica.math.stats
Correlation() - Constructor for class umcg.genetica.math.stats.Correlation
correlationToP(double, int, StudentT) - Static method in class umcg.genetica.math.stats.ZScores: Returns the two-sided p-value for a given correlation coefficient from Student's t distribution.
correlationToZ(double, int, StudentT) - Static method in class umcg.genetica.math.stats.ZScores: Returns the Z-score for a given correlation coefficient from Student's t distribution.
correlationToZScore(int) - Static method in class umcg.genetica.math.stats.Correlation
cos(double, double, double, double, double, double) - Static method in class umcg.genetica.math.Fmath
cos(double, double, double) - Static method in class umcg.genetica.math.Fmath
cos(double) - Static method in class umcg.genetica.math.Fmath
cosh(double) - Static method in class umcg.genetica.math.Fmath
cot(double) - Static method in class umcg.genetica.math.Fmath
coth(double) - Static method in class umcg.genetica.math.Fmath
countCols(Pattern) - Method in class umcg.genetica.io.text.TextFile
countLines() - Method in class umcg.genetica.io.text.TextFile
covariate(double[], double[]) - Static method in class umcg.genetica.math.stats.Correlation: Fast covariation of two double[] ToDo change correlateMeanCenteredData code to covariate code! ToDo add test
covariate(double, double, double[], double[]) - Static method in class umcg.genetica.math.stats.Correlation: Fast covariation of two double[] with their mean values ToDo change correlateMeanCenteredData code to covariate code! ToDo add test
covariateFile - Variable in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDatasetSettings
covariates - Variable in class umcg.genetica.io.binInteraction.BinaryInteractionFile
covers(double) - Static method in class umcg.genetica.math.Fmath
CREATE - Static variable in class umcg.genetica.io.bin.RandomAccessFile: Create the file rather than overwriting it.
create() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFileCreator
createBinaryInteractionFile() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFileConstructorBuilder
createDigest(String) - Static method in class com.mastfrog.util.streams.HashingInputStream
createDir(String) - Static method in class umcg.genetica.io.Gpio
createFromChrGroupedIterable(Iterable<T>, Class<T>) - Static method in class umcg.genetica.collections.intervaltree.PerChrIntervalTree: Elements must be grouped per chromosome
createIntervalTree() - Method in class umcg.genetica.io.bed.BedFile
createIntervalTree() - Method in class umcg.genetica.io.bedgraph.BedGraphFile
createIntervalTree() - Method in class umcg.genetica.io.gtf.GtfReader
createOuputDir(File) - Static method in class umcg.genetica.io.Gpio
createSNPLoader() - Method in class umcg.genetica.io.trityper.TriTyperGenotypeData
CreatSubsetBasedOnColumns(DoubleMatrixDataset<String, String>, HashSet<String>, boolean) - Static method in class umcg.genetica.math.matrix2.MatrixHandling: Filter out columns.
CreatSubsetBasedOnRows(DoubleMatrixDataset<String, String>, HashSet<String>, boolean) - Static method in class umcg.genetica.math.matrix2.MatrixHandling: Remove or filter rows.
csc(double) - Static method in class umcg.genetica.math.Fmath
csch(double) - Static method in class umcg.genetica.math.Fmath
CubicSpline - Class in umcg.genetica.math.interpolation: ******************************************************** Class CubicSpline Class for performing an interpolation using a cubic spline setTabulatedArrays and interpolate adapted, with modification to an object-oriented approach, from Numerical Recipes in C (http://www.nr.com/) WRITTEN BY: Dr Michael Thomas Flanagan DATE: May 2002 UPDATE: 29 April 2005, 17 February 2006, 21 September 2006, 4 December 2007 24 March 2008 (Thanks to Peter Neuhaus, Florida Institute for Human and Machine Cognition) 21 September 2008 14 January 2009 - point deletion and check for 3 points reordered (Thanks to Jan Sacha, Vrije Universiteit Amsterdam) 31 October 2009, 11-14 January 2010 31 August 2010 - overriding natural spline error, introduced in earlier update, corrected (Thanks to Dagmara Oszkiewicz, University of Helsinki) 2 February 2011 DOCUMENTATION: See Michael Thomas Flanagan's Java library on-line web page: http://www.ee.ucl.ac.uk/~mflanaga/java/CubicSpline.html http://www.ee.ucl.ac.uk/~mflanaga/java/ Copyright (c) 2002 - 2010 Michael Thomas Flanagan PERMISSION TO COPY: Permission to use, copy and modify this software and its documentation for NON-COMMERCIAL purposes is granted, without fee, provided that an acknowledgement to the author, Dr Michael Thomas Flanagan at www.ee.ucl.ac.uk/~mflanaga, appears in all copies and associated documentation or publications.
CubicSpline(double[], double[]) - Constructor for class umcg.genetica.math.interpolation.CubicSpline
CubicSpline(int) - Constructor for class umcg.genetica.math.interpolation.CubicSpline
cupUStoPintUK(double) - Static method in class umcg.genetica.math.Fmath

D

dash - Static variable in class umcg.genetica.text.Strings
dataEnd - Variable in class umcg.genetica.io.bin.RandomAccessFile: The offset in bytes of the end of the data in the buffer, from the start of the file.
DATASECORR - Static variable in class umcg.genetica.io.trityper.QTLTextFile
DATASETB - Static variable in class umcg.genetica.io.trityper.QTLTextFile
DATASETNAMES - Static variable in class umcg.genetica.io.trityper.QTLTextFile
DATASETSIZE - Static variable in class umcg.genetica.io.trityper.QTLTextFile
DATASETZSCORE - Static variable in class umcg.genetica.io.trityper.QTLTextFile
dataSize - Variable in class umcg.genetica.io.bin.RandomAccessFile: The size of the data stored in the buffer, in bytes.
dateToJavaMilliS(int, int, int, int, int, int) - Static method in class umcg.genetica.math.Fmath
DeepCopy - Class in umcg.genetica.methylation
DeepCopy() - Constructor for class umcg.genetica.methylation.DeepCopy
DEFAULT_BUFFER_SIZE - Static variable in class umcg.genetica.io.text.TextFile
defaultBufferSize - Static variable in class umcg.genetica.io.bin.RandomAccessFile: The default buffer size, in bytes.
degToRad(double) - Static method in class umcg.genetica.math.Fmath
Demographics - Class in umcg.genetica.text.parsing
Demographics(String) - Constructor for class umcg.genetica.text.parsing.Demographics
Dependifier - Class in umcg.genetica.gwas
Dependifier(String) - Constructor for class umcg.genetica.gwas.Dependifier
Dependifier(TriTyperGenotypeData, SNPLoader) - Constructor for class umcg.genetica.gwas.Dependifier
dependify(String[], double, int) - Method in class umcg.genetica.gwas.Dependifier
dependify(String[], String[], double, int) - Method in class umcg.genetica.gwas.Dependifier
dependifyReturnProxiesPerSNP(String[], double, int) - Method in class umcg.genetica.gwas.Dependifier
dependifyReturnProxiesPerSNP(String[], String[], double, int) - Method in class umcg.genetica.gwas.Dependifier
Descriptives - Class in umcg.genetica.math.stats
Descriptives() - Constructor for class umcg.genetica.math.stats.Descriptives
DetermineLD - Class in umcg.genetica.io.trityper.util
DetermineLD() - Constructor for class umcg.genetica.io.trityper.util.DetermineLD: Creates a new instance of DetermineLD
displayLimits() - Method in class umcg.genetica.math.interpolation.CubicSpline
dispose() - Method in class umcg.genetica.math.matrix.SymmetricByteDistanceMatrix
doesMatchFilter(GffElement) - Method in class umcg.genetica.io.gtf.GffAttributeFilter
dot - Static variable in class umcg.genetica.text.Strings
DOUBLELINE - Static variable in class umcg.genetica.console.ConsoleGUIElems
DoubleMatrixDataset<T,U> - Class in umcg.genetica.math.matrix: Deprecated.
DoubleMatrixDataset() - Constructor for class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
DoubleMatrixDataset(String) - Constructor for class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
DoubleMatrixDataset(String, DoubleMatrixDatasetAC.LoadLabels) - Constructor for class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
DoubleMatrixDataset(String, Set<T>) - Constructor for class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
DoubleMatrixDataset(String, Set<T>, DoubleMatrixDatasetAC.LoadLabels) - Constructor for class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
DoubleMatrixDataset(String, Set<T>, Set) - Constructor for class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
DoubleMatrixDataset(String, Set<T>, Set, int) - Constructor for class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
DoubleMatrixDataset(String, Set<T>, Set, DoubleMatrixDatasetAC.LoadLabels) - Constructor for class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
DoubleMatrixDataset(String, Set<T>, Set, DoubleMatrixDatasetAC.LoadLabels, int) - Constructor for class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
DoubleMatrixDataset(String, String) - Constructor for class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
DoubleMatrixDataset(double[][]) - Constructor for class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
DoubleMatrixDataset(double[][], List, List<T>) - Constructor for class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
DoubleMatrixDataset(int, int) - Constructor for class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
DoubleMatrixDataset<R extends Comparable,C extends Comparable> - Class in umcg.genetica.math.matrix2
DoubleMatrixDataset() - Constructor for class umcg.genetica.math.matrix2.DoubleMatrixDataset
DoubleMatrixDataset(int, int) - Constructor for class umcg.genetica.math.matrix2.DoubleMatrixDataset
DoubleMatrixDataset(LinkedHashMap<R, Integer>, LinkedHashMap<C, Integer>) - Constructor for class umcg.genetica.math.matrix2.DoubleMatrixDataset
DoubleMatrixDataset(DoubleMatrix2D, LinkedHashMap<R, Integer>, LinkedHashMap<C, Integer>) - Constructor for class umcg.genetica.math.matrix2.DoubleMatrixDataset
DoubleMatrixDataset(List<R>, List<C>) - Constructor for class umcg.genetica.math.matrix2.DoubleMatrixDataset
DoubleMatrixDatasetAC<T,U> - Class in umcg.genetica.math.matrix: Deprecated.
DoubleMatrixDatasetAC() - Constructor for class umcg.genetica.math.matrix.DoubleMatrixDatasetAC: Deprecated.
DoubleMatrixDatasetAC.LoadLabels - Enum in umcg.genetica.math.matrix: Deprecated.
DoubleMatrixDatasetRA<T,U> - Class in umcg.genetica.math.matrix: Deprecated.
DoubleMatrixDatasetRA(String) - Constructor for class umcg.genetica.math.matrix.DoubleMatrixDatasetRA: Deprecated.
DoubleMatrixDatasetRA(String, DoubleMatrixDatasetAC.LoadLabels) - Constructor for class umcg.genetica.math.matrix.DoubleMatrixDatasetRA: Deprecated.
DoubleMatrixDatasetRA(String, Set<T>) - Constructor for class umcg.genetica.math.matrix.DoubleMatrixDatasetRA: Deprecated.
DoubleMatrixDatasetRA(String, Set<T>, DoubleMatrixDatasetAC.LoadLabels) - Constructor for class umcg.genetica.math.matrix.DoubleMatrixDatasetRA: Deprecated.
DoubleMatrixDatasetRA(String, Set<T>, Set) - Constructor for class umcg.genetica.math.matrix.DoubleMatrixDatasetRA: Deprecated.
DoubleMatrixDatasetRA(String, Set<T>, Set, DoubleMatrixDatasetAC.LoadLabels) - Constructor for class umcg.genetica.math.matrix.DoubleMatrixDatasetRA: Deprecated.
DoubleParseTask - Class in umcg.genetica.io.concurrent
DoubleParseTask(String, int, int, int[], Set) - Constructor for class umcg.genetica.io.concurrent.DoubleParseTask
DoubleParseTask(String, int, int, int[], Set, Pattern) - Constructor for class umcg.genetica.io.concurrent.DoubleParseTask
doubleTOint(double[]) - Static method in class umcg.genetica.math.Fmath
doubleValue - Variable in class umcg.genetica.containers.StringDoubleObject
draw(String) - Method in class umcg.genetica.graphics.VennDiagram
draw(double[][][], String[], String[][], String, ViolinBoxPlot.Output, String) - Method in class umcg.genetica.graphics.ViolinBoxPlot
draw(double[][][], String[], String[][], String, ViolinBoxPlot.Output, String, boolean) - Method in class umcg.genetica.graphics.ViolinBoxPlot
drawBoxPlot(Graphics2D, int, int, int, int, double[], double, double, boolean) - Method in class umcg.genetica.graphics.ViolinBoxPlot
drawCorrelationHeatmap(double[][], String[], String[], int, int, String, Heatmap.Output) - Static method in class umcg.genetica.graphics.Heatmap: Correlation heatmap implementation Marc Jan Always use minimal value:-1 and maximum value: 1
drawDiamond(int, int, int, int) - Method in class umcg.genetica.graphics.ForestPlot
drawForrestPlot(String, String[], Double[], String, ForestPlot.Output, double[], Double, Double, int[], byte[], int[], int) - Method in class umcg.genetica.graphics.ForestPlot
drawHeatmap(double[][], String[], String[], int, int, String, Heatmap.Output) - Static method in class umcg.genetica.graphics.Heatmap: Original heatmap implementation Juha
drawMultiForrestPlot(String, String[], Double[][], String, ForestPlot.Output, double[], Double, Double, int[], byte[], int[], int) - Method in class umcg.genetica.graphics.ForestPlot
drawViolinPlot(Graphics2D, int, int, int, int, double[], double, double) - Method in class umcg.genetica.graphics.ViolinBoxPlot

E

E - Static variable in class umcg.genetica.math.Fmath
effect - Variable in class umcg.genetica.containers.SortableSNP
eigenValueDecomposition(double[][]) - Static method in class umcg.genetica.math.PCA
eigenValueDecomposition(double[][], int) - Method in class umcg.genetica.math.PCA
emptyDoubleArray - Static variable in class umcg.genetica.io.binInteraction.BinaryInteractionZscores
emptyIntArray - Static variable in class umcg.genetica.io.binInteraction.BinaryInteractionZscores
ENCODING - Static variable in class umcg.genetica.io.geofiles.ParseSoftFile
ENCODING - Static variable in class umcg.genetica.io.geofiles.ParseTextTable
ENCODING - Static variable in class umcg.genetica.io.probemapping.reading
ENCODING - Static variable in class umcg.genetica.io.text.TextFile
ENCODING - Static variable in class umcg.genetica.methylation.ParseTcgaMethylationFile
endOfFile - Variable in class umcg.genetica.io.bin.RandomAccessFile: True if we are at the end of the file.
EPSILON_0 - Static variable in class umcg.genetica.math.Fmath
EQTL - Class in umcg.genetica.io.trityper
EQTL() - Constructor for class umcg.genetica.io.trityper.EQTL
equals(Object) - Method in class umcg.genetica.collections.intervaltree.StringRange
equals(Object) - Method in class umcg.genetica.containers.Pair
equals(Object) - Method in class umcg.genetica.containers.Triple
equals(Object) - Method in class umcg.genetica.io.regulomedb.RegulomeDbEntry
equals(Object) - Method in class umcg.genetica.io.regulomedb.RegulomeDbSupportingData
equals(Object) - Method in class umcg.genetica.io.trityper.EQTL
equals(EQTL) - Method in class umcg.genetica.io.trityper.EQTL
equals(TriTyperGeneticalGenomicsDataset) - Method in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDataset
equals(UCSCDataObject) - Method in class umcg.genetica.io.ucsc.UCSCDataObject
equals(UCSCTrack) - Method in class umcg.genetica.io.ucsc.UCSCTrack
ETA_0 - Static variable in class umcg.genetica.math.Fmath
EULER_CONSTANT_GAMMA - Static variable in class umcg.genetica.math.Fmath
evToNm(double) - Static method in class umcg.genetica.math.Fmath
exists(String) - Static method in class umcg.genetica.io.Gpio
existsAndReadable(File) - Static method in class umcg.genetica.io.Gpio
Exon - Class in umcg.genetica.containers
Exon() - Constructor for class umcg.genetica.containers.Exon
export(String, String, String, String, String) - Method in class umcg.genetica.io.trityper.converters.TriTyperReferenceConcordantPedAndMapExporter
exportAllSNPs(String, String, String) - Method in class umcg.genetica.io.trityper.converters.TriTyperToDosageConverter
exportAllSNPs(String, String, boolean) - Method in class umcg.genetica.io.trityper.converters.TriTyperToPedAndMapConverter
exportFamFile(TriTyperGenotypeData, String) - Method in class umcg.genetica.io.trityper.converters.TriTyperToPedAndMapConverter
exportSubsetOfSNPs(String, String, String, String) - Method in class umcg.genetica.io.trityper.converters.TriTyperToDosageConverter
exportSubsetOfSNPs(String, String, String, String) - Method in class umcg.genetica.io.trityper.converters.TriTyperToPedAndMapConverter
ExpressionDataset - Class in umcg.genetica.legacy
ExpressionDataset() - Constructor for class umcg.genetica.legacy.ExpressionDataset
expressionLocation - Variable in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDatasetSettings
expressionplatform - Variable in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDatasetSettings
exsec(double) - Static method in class umcg.genetica.math.Fmath
extrapolateZScore(int, int, double) - Static method in class umcg.genetica.math.stats.ZScores

F

F_FARADAY - Static variable in class umcg.genetica.math.Fmath
factorial(int) - Static method in class umcg.genetica.math.Fmath
factorial(long) - Static method in class umcg.genetica.math.Fmath
factorial(BigInteger) - Static method in class umcg.genetica.math.Fmath
factorial(double) - Static method in class umcg.genetica.math.Fmath
factorial(BigDecimal) - Static method in class umcg.genetica.math.Fmath
fahrenToCelsius(double) - Static method in class umcg.genetica.math.Fmath
FDRUtils - Class in umcg.genetica.math.stats
FDRUtils.AbsoluteValues - Enum in umcg.genetica.math.stats
FDRUtils.CloneArrays - Enum in umcg.genetica.math.stats
FDRUtils.SortArrays - Enum in umcg.genetica.math.stats
Features - Class in umcg.genetica.ensembl
Features() - Constructor for class umcg.genetica.ensembl.Features
file - Variable in class umcg.genetica.io.bin.RandomAccessFile: The underlying java.io.RandomAccessFile.
file - Variable in class umcg.genetica.io.text.TextFile
fileName - Variable in class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
fileName - Variable in class umcg.genetica.math.matrix.DoubleMatrixDatasetRA: Deprecated.
filePosition - Variable in class umcg.genetica.io.bin.RandomAccessFile: The offset in bytes from the file start, of the next read or write operation.
filter - Variable in class umcg.genetica.io.gtf.GffAttributeFilter
FilterCols(DoubleMatrixDataset<String, String>, HashSet<String>) - Static method in class umcg.genetica.math.matrix.MatrixHandling
FilterRows(DoubleMatrixDataset<String, String>, HashSet<String>) - Static method in class umcg.genetica.math.matrix.MatrixHandling: Remove rows without correct mapping known on forehand
finalizeWriting() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
FinalReportToTriTyper - Class in umcg.genetica.io.trityper.converters
FinalReportToTriTyper(String, String, boolean, String, String) - Constructor for class umcg.genetica.io.trityper.converters.FinalReportToTriTyper: Starts parsing a genotype report file, which can be in different formats.
findProxiesForSNP(String, double, int) - Method in class umcg.genetica.gwas.Dependifier
FisherExactTest - Class in umcg.genetica.math.stats
FisherExactTest() - Constructor for class umcg.genetica.math.stats.FisherExactTest: Creates a new instance of FisherExactTest
fixLinkedHashes(LinkedHashMap<String, Integer>) - Static method in class umcg.genetica.math.matrix2.MatrixHandling
flipalleles(String, String, String, String) - Static method in class umcg.genetica.io.trityper.util.BaseAnnot
floatTOdouble(float[]) - Static method in class umcg.genetica.math.Fmath
fluidOunceUKtoUS(double) - Static method in class umcg.genetica.math.Fmath
fluidOunceUStoUK(double) - Static method in class umcg.genetica.math.Fmath
flush() - Method in class umcg.genetica.io.bin.RandomAccessFile: Copy the contents of the buffer to the disk.
flush() - Method in class umcg.genetica.io.text.TextFile
flush() - Method in class umcg.genetica.io.trityper.bin.BinaryGZipFloatMatrix
Fmath - Class in umcg.genetica.math
Fmath() - Constructor for class umcg.genetica.math.Fmath
footToMetre(double) - Static method in class umcg.genetica.math.Fmath
ForestPlot - Class in umcg.genetica.graphics
ForestPlot() - Constructor for class umcg.genetica.graphics.ForestPlot
ForestPlot.Output - Enum in umcg.genetica.graphics
formatAsDirectory(String) - Static method in class umcg.genetica.io.Gpio
forwardslash - Static variable in class umcg.genetica.text.Strings
frequencyToRadialFrequency(double) - Static method in class umcg.genetica.math.Fmath

G

G - Static variable in class umcg.genetica.io.trityper.util.BaseAnnot
gallonPerMileToLitrePerKm(double) - Static method in class umcg.genetica.math.Fmath
gallonToLitre(double) - Static method in class umcg.genetica.math.Fmath
gallonUKtoUS(double) - Static method in class umcg.genetica.math.Fmath
gallonUStoUK(double) - Static method in class umcg.genetica.math.Fmath
Gene - Class in umcg.genetica.containers
Gene() - Constructor for class umcg.genetica.containers.Gene
GenomicBoundaries<V> - Class in umcg.genetica.genomicboundaries
GenomicBoundaries(String) - Constructor for class umcg.genetica.genomicboundaries.GenomicBoundaries: Constructor for building Genomic Boundaries from a file.
GenomicBoundaries() - Constructor for class umcg.genetica.genomicboundaries.GenomicBoundaries: Empty constructor that only creates an empty structure for saving Genomic Boundaries.
GenomicBoundaries(String, int) - Constructor for class umcg.genetica.genomicboundaries.GenomicBoundaries
GenomicBoundariesIterator<V> - Class in umcg.genetica.genomicboundaries
GenomicBoundariesIterator(HashMap<String, TreeMap<Integer, ArrayList<GenomicBoundary<V>>>>) - Constructor for class umcg.genetica.genomicboundaries.GenomicBoundariesIterator
GenomicBoundariesSimple - Class in umcg.genetica.genomicboundaries
GenomicBoundariesSimple(String) - Constructor for class umcg.genetica.genomicboundaries.GenomicBoundariesSimple
GenomicBoundariesSimple(String, int) - Constructor for class umcg.genetica.genomicboundaries.GenomicBoundariesSimple
GenomicBoundary<V> - Class in umcg.genetica.genomicboundaries
GenomicBoundary(String, Integer, int) - Constructor for class umcg.genetica.genomicboundaries.GenomicBoundary
GenomicBoundary(String, Integer, int, V) - Constructor for class umcg.genetica.genomicboundaries.GenomicBoundary
GenomicRange - Interface in umcg.genetica.variantAnnotator
genotypeLocation - Variable in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDatasetSettings
genotypeToExpressionCoupling - Variable in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDatasetSettings
get(String, int) - Method in class umcg.genetica.collections.ChrPosMap
get(String, Integer) - Method in class umcg.genetica.collections.ChrPosTreeMap
get(int) - Method in class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
get(int, int) - Method in class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
get(int) - Method in class umcg.genetica.math.matrix.DoubleMatrixDatasetAC: Deprecated.
get(int, int) - Method in class umcg.genetica.math.matrix.DoubleMatrixDatasetAC: Deprecated.
get(int) - Method in class umcg.genetica.math.matrix.DoubleMatrixDatasetRA: Deprecated.
get(int, int) - Method in class umcg.genetica.math.matrix.DoubleMatrixDatasetRA: Deprecated.
get(int, int) - Method in class umcg.genetica.math.matrix.SymmetricByteDistanceMatrix
get(int, int) - Method in class umcg.genetica.math.matrix.SymmetricShortDistanceMatrix
getAbsolutePath() - Method in class umcg.genetica.io.pileup.PileupFile
getAccession() - Method in class umcg.genetica.methylation.SoftfileAnnotation
getActualMappingPosition(Integer) - Method in class umcg.genetica.io.trityper.probeannotation.ProbeTranslation
getAllele1() - Method in class umcg.genetica.io.trityper.SNP
getAllele1(int, int) - Method in class umcg.genetica.io.trityper.WGAFileMatrixGenotype
getAllele2() - Method in class umcg.genetica.io.trityper.SNP
getAllele2(int, int) - Method in class umcg.genetica.io.trityper.WGAFileMatrixGenotype
getAlleleAssessed() - Method in class umcg.genetica.io.trityper.EQTL
getAlleleAverageQualities() - Method in class umcg.genetica.io.pileup.PileupEntry
getAlleleAverageQuality(Allele) - Method in class umcg.genetica.io.pileup.PileupEntry
getAlleleCount(Allele) - Method in class umcg.genetica.io.pileup.PileupEntry
getAlleleCounts() - Method in class umcg.genetica.io.pileup.PileupEntry
getAlleleFreq() - Method in class umcg.genetica.io.trityper.SNP
getAlleleItr() - Method in class umcg.genetica.io.trityper.SNP
getAlleles() - Method in class umcg.genetica.io.trityper.bin.BinaryResultSNP
getAlleles() - Method in class umcg.genetica.io.trityper.EQTL
getAlleles() - Method in class umcg.genetica.io.trityper.SNP
getAllelesDescription(byte[]) - Static method in class umcg.genetica.io.trityper.util.BaseAnnot
getAllPairsShortestPath() - Method in class umcg.genetica.math.matrix.SymmetricByteDistanceMatrix
getAllPairsShortestPath() - Method in class umcg.genetica.math.matrix.SymmetricShortDistanceMatrix
getAltAllele() - Method in interface umcg.genetica.io.binInteraction.variant.BinaryInteractionVariant
getAltAllele() - Method in class umcg.genetica.io.binInteraction.variant.BinaryInteractionVariantAbstract
getAnnotation() - Method in class umcg.genetica.containers.Gene
getAnnotation() - Method in class umcg.genetica.genomicboundaries.GenomicBoundary
getAnnotation() - Method in class umcg.genetica.io.trityper.bin.BinaryResultProbe
getAnnotation() - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
getAnnotationInformation() - Method in class umcg.genetica.methylation.SoftfileAnnotation
getASquared(double[]) - Static method in class umcg.genetica.math.stats.AndersonDarling
getASquared(double[], AndersonDarling.IS_DATA_NORMALIZED) - Static method in class umcg.genetica.math.stats.AndersonDarling
getAssessedAllele() - Method in class umcg.genetica.io.trityper.bin.BinaryResultSNP
getAssociatedTraits() - Method in class umcg.genetica.io.gwascatalog.GWASSNP
getAssociatedTraitsArray() - Method in class umcg.genetica.io.gwascatalog.GWASSNP
getAttributes() - Method in class umcg.genetica.io.gtf.GffElement
getAttributeValue(String) - Method in class umcg.genetica.io.gtf.GffElement
getAUC(double[], double[]) - Static method in class umcg.genetica.math.stats.AUC
getAUC() - Method in class umcg.genetica.math.stats.WilcoxonMannWhitney
getAverageSNPSize(int) - Method in class umcg.genetica.io.trityper.BufferedSNPLoader
getAverageSNPSize(int) - Method in class umcg.genetica.io.trityper.SNPLoader
getBeta() - Method in class umcg.genetica.io.trityper.EQTL
getBins(double[], double, double, int) - Static method in class umcg.genetica.math.stats.Binning
getBoudaryCount() - Method in class umcg.genetica.genomicboundaries.GenomicBoundaries: This method returns the count of Boundary objects.
getBoundary(String, int, int) - Method in class umcg.genetica.genomicboundaries.GenomicBoundaries: This method returns a Boundary object from a chromosome at a specific position.
getBoundary(String, int) - Method in class umcg.genetica.genomicboundaries.GenomicBoundariesSimple
getBoundaryCountChromosome(String) - Method in class umcg.genetica.genomicboundaries.GenomicBoundaries
getChr() - Method in interface umcg.genetica.io.binInteraction.gene.BinaryInteractionGene
getChr() - Method in class umcg.genetica.io.binInteraction.gene.BinaryInteractionGeneAbstract
getChr() - Method in interface umcg.genetica.io.binInteraction.variant.BinaryInteractionVariant
getChr() - Method in class umcg.genetica.io.binInteraction.variant.BinaryInteractionVariantAbstract
getChr() - Method in class umcg.genetica.io.gwascatalog.GWASSNP
getChr() - Method in class umcg.genetica.io.pileup.PileupEntry
getChr() - Method in class umcg.genetica.io.regulomedb.RegulomeDbEntry
getChr() - Method in class umcg.genetica.io.trityper.bin.BinaryResultProbe
getChr() - Method in class umcg.genetica.io.trityper.bin.BinaryResultSNP
getChr() - Method in class umcg.genetica.io.trityper.ProbeAnnotation
getChr() - Method in class umcg.genetica.io.trityper.SNP
getChr() - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
getChr(int) - Method in class umcg.genetica.io.trityper.TriTyperGenotypeData
getChr(String) - Method in class umcg.genetica.io.trityper.TriTyperSNPMappings
getChr(Integer) - Method in class umcg.genetica.io.trityper.TriTyperSNPMappings
getChr() - Method in class umcg.genetica.io.ucsc.UCSCDataObject
getChrEnd() - Method in class umcg.genetica.io.trityper.ProbeAnnotation
getChromosome() - Method in class umcg.genetica.genomicboundaries.GenomicBoundary
getChromosomeHash() - Method in class umcg.genetica.ensembl.Features
getChromosomes() - Method in class umcg.genetica.genomicboundaries.GenomicBoundaries
getChromosomes() - Method in class umcg.genetica.genomicboundaries.GenomicBoundariesSimple
getChromosomes() - Method in class umcg.genetica.io.fasta.ReferenceGenomeFasta
getChrPos() - Method in class umcg.genetica.io.regulomedb.RegulomeDbEntry
getChrpos() - Method in class umcg.genetica.io.trityper.bin.BinaryResultSNP
getChrPos() - Method in class umcg.genetica.io.trityper.SNP
getChrPos(int) - Method in class umcg.genetica.io.trityper.TriTyperGenotypeData
getChrPos(String) - Method in class umcg.genetica.io.trityper.TriTyperSNPMappings
getChrPos(Integer) - Method in class umcg.genetica.io.trityper.TriTyperSNPMappings
getChrPosIterator() - Method in class umcg.genetica.collections.ChrPosTreeMap: not tested
getChrPositions(String) - Method in class umcg.genetica.collections.ChrPosTreeMap
getChrs() - Method in class umcg.genetica.collections.ChrPosTreeMap
getChrStart() - Method in class umcg.genetica.io.trityper.ProbeAnnotation
getChrStart() - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
getChrStop() - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
getCleanName() - Method in class umcg.genetica.io.gwascatalog.GWASTrait
getCohortCount() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
getCohortCount() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionQtlZscores
getCohortCount() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionZscores
getCohorts() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
getColNames() - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
getColNameToId() - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
getColObjects() - Method in class umcg.genetica.math.matrix2.DoubleMatrixDataset
getColumnObjectsOnly(String) - Static method in class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
getColumnObjectsOnly(String) - Static method in class umcg.genetica.math.matrix.DoubleMatrixDatasetRA: Deprecated.
getComplement(byte) - Static method in class umcg.genetica.io.trityper.util.BaseAnnot
getComplement(String) - Static method in class umcg.genetica.io.trityper.util.BaseAnnot
getContigs() - Method in class umcg.genetica.ncbi.dbsnp.SNPAnnotation
getCorrelationFromDistance(int) - Method in class umcg.genetica.math.matrix.SymmetricShortDistanceMatrix
getCorrelations() - Method in class umcg.genetica.io.trityper.EQTL
getCovariateCount() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
getCovariateData() - Method in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDataset
getCovariateName() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionQueryResult
getCovariates() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
getCr() - Method in class umcg.genetica.io.trityper.bin.BinaryResultSNP
getCR() - Method in class umcg.genetica.io.trityper.SNP
getCreationDataEpoch() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
getCreationDataTimeString() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
getData() - Method in class umcg.genetica.io.ucsc.UCSCTrack
getDataMatrixPCScores(double[][], int, int) - Method in class umcg.genetica.math.PCA
getDatasets() - Method in class umcg.genetica.io.trityper.EQTL
getDatasetsSamples() - Method in class umcg.genetica.io.trityper.EQTL
getDatasetZScores() - Method in class umcg.genetica.io.trityper.EQTL
getDeriv() - Method in class umcg.genetica.math.interpolation.CubicSpline
getDescriptives(double[], double[]) - Static method in class umcg.genetica.math.stats.TheilSen: Calculates Theil-Sen estimation for given arrays.
getDiff(EQTL) - Method in class umcg.genetica.io.trityper.EQTL
getDigest() - Method in class com.mastfrog.util.streams.HashingInputStream
getDigest() - Method in class com.mastfrog.util.streams.HashingOutputStream
getDistance(double) - Method in class umcg.genetica.math.matrix.SymmetricByteDistanceMatrix
getDistance(double) - Method in class umcg.genetica.math.matrix.SymmetricShortDistanceMatrix
getDistanceFromCorrelation(double) - Method in class umcg.genetica.math.matrix.SymmetricShortDistanceMatrix: The distance measure in short ranges from 0 to 65.000.
getDosage(int, int) - Method in class umcg.genetica.io.trityper.WGAFileMatrixImputedDosage
getDosageFileName() - Method in class umcg.genetica.io.trityper.TriTyperGenotypeData
getDosageMAF() - Method in class umcg.genetica.io.trityper.SNP
getDosageValues() - Method in class umcg.genetica.io.trityper.SNP
getEigenValueVar(double[], int) - Static method in class umcg.genetica.math.PCA
getEigenVector(EigenvalueDecomposition, double[], int) - Static method in class umcg.genetica.math.PCA
getEigenVector(EigenvalueDecomposition, int) - Static method in class umcg.genetica.math.PCA
getEigenVectorSVD(SingularValueDecomposition, double[], int) - Static method in class umcg.genetica.math.PCA
getElement(R, C) - Method in class umcg.genetica.math.matrix2.DoubleMatrixDataset: Get specific element.
getElement(int, int) - Method in class umcg.genetica.math.matrix2.DoubleMatrixDataset: Get specific element.
getElementsOverlappingQuery(int) - Method in class umcg.genetica.collections.intervaltree.IntervalTree
getEnd() - Method in interface umcg.genetica.collections.intervaltree.Range: Inclusive
getEnd() - Method in class umcg.genetica.collections.intervaltree.StringRange
getEnd() - Method in class umcg.genetica.containers.Exon
getEnd() - Method in class umcg.genetica.containers.Gene
getEnd() - Method in class umcg.genetica.containers.Transcript
getEnd() - Method in class umcg.genetica.io.bed.BedEntry
getEnd() - Method in class umcg.genetica.io.bedgraph.BedGraphEntry
getEnd() - Method in interface umcg.genetica.io.binInteraction.gene.BinaryInteractionGene
getEnd() - Method in class umcg.genetica.io.binInteraction.gene.BinaryInteractionGeneAbstract
getEnd() - Method in class umcg.genetica.io.gtf.GffElement
getEndExclusive() - Method in class umcg.genetica.io.bed.BedEntry
getEndExclusive() - Method in class umcg.genetica.io.bedgraph.BedGraphEntry
getEQtlIterator() - Method in class umcg.genetica.io.trityper.QTLTextFile
getExon(String) - Method in class umcg.genetica.ensembl.Features
getExonHash() - Method in class umcg.genetica.ensembl.Features
getExons() - Method in class umcg.genetica.containers.Transcript
getExonsRanked() - Method in class umcg.genetica.containers.Transcript
getExpressionData() - Method in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDataset
getExpressionToGenotypeIdArray() - Method in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDataset
getExpressionToGenotypeIdArrayShort() - Method in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDataset
getExpressionToGenotypeIdHash() - Method in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDataset
getFC() - Method in class umcg.genetica.io.trityper.EQTL
getFD() - Method in class umcg.genetica.io.bin.RandomAccessFile: Returns the opaque file descriptor object associated with this file.
getFDR() - Method in class umcg.genetica.io.trityper.EQTL
getFeature() - Method in class umcg.genetica.io.gtf.GffElement
getFileDescription() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
getFileName(String) - Static method in class umcg.genetica.io.Gpio
getFileName() - Method in class umcg.genetica.io.text.TextFile
getFilePointer() - Method in class umcg.genetica.io.bin.RandomAccessFile: Returns the current position in the file, where the next read or write will occur.
getFileSeparator() - Static method in class umcg.genetica.io.Gpio
getFileSize(String) - Static method in class umcg.genetica.io.Gpio
getFisherLeftTail() - Method in class umcg.genetica.math.stats.FisherExactTest
getFisherPValue(int, int, int, int) - Method in class umcg.genetica.math.stats.FisherExactTest
getFisherRightTail() - Method in class umcg.genetica.math.stats.FisherExactTest
getFrame() - Method in class umcg.genetica.io.gtf.GffElement
getFullComplement(String) - Static method in class umcg.genetica.io.trityper.util.BaseAnnot
getFullTraitsForCertainSnps(String) - Method in class umcg.genetica.io.gwascatalog.GWASCatalog
getGCScore(int, int) - Method in class umcg.genetica.io.trityper.WGAFileMatrixRawData
getGene(String) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
getGene(int) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
getGeneCount() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
getGeneCount() - Method in interface umcg.genetica.io.binInteraction.variant.BinaryInteractionVariant
getGeneCount() - Method in class umcg.genetica.io.binInteraction.variant.BinaryInteractionVariantCreator
getGeneCount() - Method in class umcg.genetica.io.binInteraction.variant.BinaryInteractionVariantStatic
getGeneHash() - Method in class umcg.genetica.ensembl.Features
getGeneName() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionQueryResult
getGenePointers() - Method in interface umcg.genetica.io.binInteraction.variant.BinaryInteractionVariant
getGenePointers() - Method in class umcg.genetica.io.binInteraction.variant.BinaryInteractionVariantCreator
getGenePointers() - Method in class umcg.genetica.io.binInteraction.variant.BinaryInteractionVariantStatic
getGenes() - Method in class umcg.genetica.containers.Chromosome
getGenes() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
getGenesForPathway(String) - Method in class umcg.genetica.io.gmt.GMTFile
getGenesHash() - Method in class umcg.genetica.containers.Chromosome
getGenomicBoundaries(String) - Method in class umcg.genetica.genomicboundaries.GenomicBoundaries: Returns the GenomicBoundaries
getGenomicBoundaries() - Method in class umcg.genetica.genomicboundaries.GenomicBoundaries: Returns the GenomicBoundaries
getGenomicBoundariesMap(String) - Method in class umcg.genetica.genomicboundaries.GenomicBoundaries: Returns a TreeMap> if the provided chromosome is present with genomicsBoundaries.
getGenotypeData() - Method in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDataset
getGenotypeFileName() - Method in class umcg.genetica.io.trityper.TriTyperGenotypeData
getGenotypeFreq() - Method in class umcg.genetica.io.trityper.SNP
getGenotypes() - Method in class umcg.genetica.io.trityper.SNP
getGenotypeToExpressionCouplings() - Method in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDataset
getGenotypeToExpressionIdHash() - Method in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDataset
getGlobalThreshold(double[][], double[][], double, FDRUtils.CloneArrays, FDRUtils.SortArrays, FDRUtils.AbsoluteValues) - Static method in class umcg.genetica.math.stats.FDRUtils: Returns the threshold value in the whole of given real data matrix that corresponds to the given false discovery rate against the null distribution from given permuted data matrix.
getGlobalThreshold(double[][], double[][][], double, FDRUtils.CloneArrays, FDRUtils.SortArrays, FDRUtils.AbsoluteValues) - Static method in class umcg.genetica.math.stats.FDRUtils: Returns the threshold value in the whole of given real data matrix that corresponds to the given false discovery rate against the null distribution from given permuted data matrices.
getHashAsString() - Method in class com.mastfrog.util.streams.HashingInputStream
getHashAsString() - Method in class com.mastfrog.util.streams.HashingOutputStream
getHashCols() - Method in class umcg.genetica.math.matrix2.DoubleMatrixDataset
getHashRows() - Method in class umcg.genetica.math.matrix2.DoubleMatrixDataset
getHwe() - Method in class umcg.genetica.io.trityper.bin.BinaryResultSNP
getHWEP() - Method in class umcg.genetica.io.trityper.SNP
getId() - Method in class umcg.genetica.io.gwascatalog.GWASSNP
getId() - Method in class umcg.genetica.io.trityper.bin.BinaryResultProbe
getId() - Method in class umcg.genetica.io.trityper.bin.BinaryResultSNP
getId() - Method in class umcg.genetica.io.trityper.SNP
getIndexOfFirstNaN(double[][]) - Static method in class umcg.genetica.math.matrix.MatrixTools
getIndexOfFirstNaN(DoubleMatrix2D) - Static method in class umcg.genetica.math.matrix2.MatrixTools
getIndexOfFirstNegative(double[][]) - Static method in class umcg.genetica.math.matrix.MatrixTools
getIndexOfFirstNegative(DoubleMatrix2D) - Static method in class umcg.genetica.math.matrix2.MatrixTools
getIndexOfFirstZero(double[][]) - Static method in class umcg.genetica.math.matrix.MatrixTools
getIndexOfFirstZero(DoubleMatrix2D) - Static method in class umcg.genetica.math.matrix2.MatrixTools
getIndexOfFirstZeroIgnoreDiagonal(double[][]) - Static method in class umcg.genetica.math.matrix.MatrixTools
getIndexOfFirstZeroIgnoreDiagonal(DoubleMatrix2D) - Static method in class umcg.genetica.math.matrix2.MatrixTools
getIndexOfGenePointer(int) - Method in interface umcg.genetica.io.binInteraction.variant.BinaryInteractionVariant
getIndexOfGenePointer(int) - Method in class umcg.genetica.io.binInteraction.variant.BinaryInteractionVariantCreator
getIndexOfGenePointer(int) - Method in class umcg.genetica.io.binInteraction.variant.BinaryInteractionVariantStatic
getIndexOfMin(double[]) - Static method in class umcg.genetica.util.Primitives
getIndexOfVariantPointer(int) - Method in interface umcg.genetica.io.binInteraction.gene.BinaryInteractionGene
getIndexOfVariantPointer(int) - Method in class umcg.genetica.io.binInteraction.gene.BinaryInteractionGeneCreator
getIndexOfVariantPointer(int) - Method in class umcg.genetica.io.binInteraction.gene.BinaryInteractionGeneStatic
getIndividualId(String) - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
getIndividualId(String) - Method in class umcg.genetica.io.trityper.TriTyperGenotypeData
getIndividuals() - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
getIndividuals() - Method in class umcg.genetica.io.trityper.TriTyperGenotypeData
getIndividualToId() - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
getIndividualToId() - Method in class umcg.genetica.io.trityper.TriTyperGenotypeData
getInteractionFile() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
getInteractionReadBufferLoaded() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
getInteractionWriteBufferFlushed() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
getInteractionZscores() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionQueryResult
getInteractionZscoresRead() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
getInteractionZscoresSet() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
getIsCase() - Method in class umcg.genetica.io.trityper.TriTyperGenotypeData
getIsFemale() - Method in class umcg.genetica.io.trityper.TriTyperGenotypeData
getIsIncluded() - Method in class umcg.genetica.io.trityper.TriTyperGenotypeData
getISq(Double[], int[]) - Static method in class umcg.genetica.math.stats.Heterogeneity
getISq(double[], int[]) - Static method in class umcg.genetica.math.stats.Heterogeneity
getKSP(double[], double[]) - Static method in class umcg.genetica.math.stats.KolmogorovSmirnov: Calculates a 2-sample Kolmogorov-Smirnov p-value.
getKSZ(double[], double[]) - Static method in class umcg.genetica.math.stats.KolmogorovSmirnov: Calculates a 2-sample Kolmogorov-Smirnov Z value.
getLD(SNP, SNP, TriTyperGenotypeData, int, boolean) - Method in class umcg.genetica.io.trityper.util.DetermineLD
getLeft() - Method in class umcg.genetica.containers.Pair
getLeft() - Method in class umcg.genetica.containers.Triple
getLength() - Method in class umcg.genetica.containers.Exon
getLength() - Method in class umcg.genetica.containers.Transcript
getLength(boolean) - Method in class umcg.genetica.genomicboundaries.GenomicBoundary
getLimits() - Method in class umcg.genetica.math.interpolation.CubicSpline
getLinearRegressionCoefficients(double[], double[]) - Static method in class umcg.genetica.math.stats.Regression
getListOfFiles(String, String, String, String) - Static method in class umcg.genetica.io.Gpio
getListOfFiles(String, String, String) - Static method in class umcg.genetica.io.Gpio
getListOfFiles(String, String) - Static method in class umcg.genetica.io.Gpio
getListOfFiles(String) - Static method in class umcg.genetica.io.Gpio
getLoci() - Method in class umcg.genetica.io.gwascatalog.GWASCatalog
getLociForCertainKey(String) - Method in class umcg.genetica.io.gwascatalog.GWASCatalog
getLocus() - Method in class umcg.genetica.io.gwascatalog.GWASSNP
getLocusToObj() - Method in class umcg.genetica.io.gwascatalog.GWASCatalog
getM_location() - Method in class umcg.genetica.io.trityper.bin.BinaryResultDataset
getM_name() - Method in class umcg.genetica.io.trityper.bin.BinaryResultDataset
getMaf() - Method in class umcg.genetica.io.trityper.bin.BinaryResultSNP
getMAF() - Method in class umcg.genetica.io.trityper.SNP
getMappedGenes() - Method in class umcg.genetica.io.gwascatalog.GWASTrait
getMappedGenesForCertainKey(String) - Method in class umcg.genetica.io.gwascatalog.GWASCatalog
getMatrix() - Method in class umcg.genetica.io.trityper.bin.BinaryResultDataset
getMatrix() - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
getMatrix() - Method in class umcg.genetica.math.matrix2.DoubleMatrixDataset
getMaxfloat() - Method in class umcg.genetica.io.trityper.bin.BinaryResultDataset
getMaxNrSamples() - Method in class umcg.genetica.io.trityper.bin.BinaryResultDataset
getMaxNrSamples() - Method in class umcg.genetica.io.trityper.bin.BinaryResultSNPSummary
getMean() - Method in class umcg.genetica.io.ucsc.UCSCTrack
getMeshTerms() - Method in class umcg.genetica.methylation.SoftfileAnnotation
getMetaBeta() - Method in class umcg.genetica.io.trityper.EQTL
getMetaZscore() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionQtlZscores
getMiddle() - Method in class umcg.genetica.containers.Triple
getMidpoint() - Method in class umcg.genetica.io.trityper.bin.BinaryResultProbe
getMinfloat() - Method in class umcg.genetica.io.trityper.bin.BinaryResultDataset
getMinimumBaseQuality() - Method in class umcg.genetica.io.pileup.PileupEntry
getMinorAllele() - Method in class umcg.genetica.io.trityper.bin.BinaryResultSNP
getMinorAllele() - Method in class umcg.genetica.io.trityper.SNP
getName() - Method in class umcg.genetica.containers.Chromosome
getName() - Method in class umcg.genetica.containers.Exon
getName() - Method in class umcg.genetica.containers.Gene
getName() - Method in class umcg.genetica.containers.Transcript
getName() - Method in class umcg.genetica.io.bed.BedEntry
getName() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionCohort
getName() - Method in interface umcg.genetica.io.binInteraction.gene.BinaryInteractionGene
getName() - Method in class umcg.genetica.io.binInteraction.gene.BinaryInteractionGeneAbstract
getName() - Method in interface umcg.genetica.io.binInteraction.variant.BinaryInteractionVariant
getName() - Method in class umcg.genetica.io.binInteraction.variant.BinaryInteractionVariantAbstract
getName() - Method in class umcg.genetica.io.gwascatalog.GWASSNP
getName() - Method in class umcg.genetica.io.gwascatalog.GWASTrait
getName() - Method in class umcg.genetica.io.trityper.bin.BinaryResultProbe
getName() - Method in class umcg.genetica.io.trityper.bin.BinaryResultSNP
getName() - Method in class umcg.genetica.io.trityper.SNP
getName() - Method in class umcg.genetica.io.ucsc.UCSCTrack
getNextRow() - Method in class umcg.genetica.math.matrix.DoubleMatrixDatasetRA: Deprecated.
getNrCalled() - Method in class umcg.genetica.io.trityper.SNP
getNrSignificant(double[][], double, FDRUtils.SortArrays, FDRUtils.AbsoluteValues) - Static method in class umcg.genetica.math.stats.FDRUtils: Calculates the number of significant Z-scores per each row in the given Z-score matrix.
getNrSignificant(double[][], double[], FDRUtils.CloneArrays, FDRUtils.SortArrays, FDRUtils.AbsoluteValues) - Static method in class umcg.genetica.math.stats.FDRUtils
getNucleotide(String, long) - Method in class umcg.genetica.io.fasta.ReferenceGenomeFasta
getNumIndividuals() - Method in class umcg.genetica.io.trityper.BufferedSNPLoader
getNumIndividuals() - Method in class umcg.genetica.io.trityper.SNPLoader
getNumProbes() - Method in class umcg.genetica.io.trityper.bin.BinaryResultDataset
getNumProbes() - Method in class umcg.genetica.io.trityper.probeannotation.ProbeTranslation
getNumsamples() - Method in class umcg.genetica.io.trityper.bin.BinaryResultSNP
getNumSNPs() - Method in class umcg.genetica.io.trityper.TriTyperSNPMappings
getOriginalProbeMean() - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
getOriginalProbeVariance() - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
getP(double[], AndersonDarling.IS_DATA_NORMALIZED) - Static method in class umcg.genetica.math.stats.AndersonDarling
getP(double, int) - Static method in class umcg.genetica.math.stats.AndersonDarling
getP(int, double) - Static method in class umcg.genetica.math.stats.ChiSquare
getParentChromosome() - Method in class umcg.genetica.containers.Exon
getParentChromosome() - Method in class umcg.genetica.containers.Gene
getParentDir(String) - Static method in class umcg.genetica.io.Gpio
getParentGene() - Method in class umcg.genetica.containers.Transcript
getParentTranscript() - Method in class umcg.genetica.containers.Exon
getPathways() - Method in class umcg.genetica.io.gmt.GMTFile
getPathwayToGenes() - Method in class umcg.genetica.io.gmt.GMTFile
getPos() - Method in interface umcg.genetica.io.binInteraction.variant.BinaryInteractionVariant
getPos() - Method in class umcg.genetica.io.binInteraction.variant.BinaryInteractionVariantAbstract
getPos() - Method in class umcg.genetica.io.pileup.PileupEntry
getPosition() - Method in class umcg.genetica.io.gwascatalog.GWASSNP
getPositionEnd() - Method in class umcg.genetica.io.ucsc.UCSCDataObject
getPositionStart() - Method in class umcg.genetica.io.ucsc.UCSCDataObject
getProbabilityKolmogorovSmirnov(double, double, double) - Static method in class umcg.genetica.math.stats.KolmogorovSmirnov
getProbe() - Method in class umcg.genetica.io.trityper.EQTL
getProbeAnnotation() - Method in class umcg.genetica.io.trityper.ProbeAnnotation
getProbeChr() - Method in class umcg.genetica.io.trityper.EQTL
getProbeChr(int) - Method in class umcg.genetica.io.trityper.probeannotation.ProbeTranslation
getProbeChrPos() - Method in class umcg.genetica.io.trityper.EQTL
getProbeChrPos(int) - Method in class umcg.genetica.io.trityper.probeannotation.ProbeTranslation
getProbeHUGO() - Method in class umcg.genetica.io.trityper.EQTL
getProbeId(String) - Method in class umcg.genetica.io.trityper.probeannotation.ProbeTranslation
getProbeMean() - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
getProbeMeans() - Method in class umcg.genetica.io.trityper.EQTL
getProbes() - Method in class umcg.genetica.io.trityper.bin.BinaryResultDataset
getProbes() - Method in class umcg.genetica.io.trityper.ProbeAnnotation
getProbes() - Method in class umcg.genetica.io.trityper.probeannotation.ProbeTranslation
getProbes() - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
getProbeSymbol(int) - Method in class umcg.genetica.io.trityper.probeannotation.ProbeTranslation
getProbeToId() - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
getProbeToProbeId() - Method in class umcg.genetica.io.trityper.ProbeAnnotation
getProbeTranslation(String, String, String) - Method in class umcg.genetica.io.trityper.probeannotation.ProbeTranslation
getProbeTranslationTable() - Method in class umcg.genetica.io.trityper.probeannotation.ProbeTranslation
getProbeVariance() - Method in class umcg.genetica.io.trityper.EQTL
getProbeVariance() - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
getProtein() - Method in class umcg.genetica.containers.Transcript
getPublicationToObj() - Method in class umcg.genetica.io.gwascatalog.GWASCatalog
getPublishedIn() - Method in class umcg.genetica.io.gwascatalog.GWASSNP
getPvalue() - Method in class umcg.genetica.io.trityper.EQTL
getPValue(int) - Method in class umcg.genetica.math.matrix.SymmetricByteDistanceMatrix
getPValue(int) - Method in class umcg.genetica.math.matrix.SymmetricShortDistanceMatrix
getPvalueAbs() - Method in class umcg.genetica.io.trityper.EQTL
getPValueAssociatedWithTrait(GWASSNP, GWASTrait) - Method in class umcg.genetica.io.gwascatalog.GWASPublication
getPValueAssociatedWithTrait(GWASTrait) - Method in class umcg.genetica.io.gwascatalog.GWASSNP
getQtlReadBufferLoaded() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
getQtlWriteBufferFlushed() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
getQtlZscores() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionQueryResult
getQtlZscoresRead() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
getQtlZscoresSet() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
getQuick(long) - Method in class umcg.genetica.io.fasta.LargeByteArray: Get value at index.
getR(int, int) - Method in class umcg.genetica.io.trityper.WGAFileMatrixRawData
getRawData() - Method in class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
getRawDataTransposed() - Method in class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
getReadDepth() - Method in class umcg.genetica.io.pileup.PileupEntry
getRealEigenvalues(EigenvalueDecomposition) - Static method in class umcg.genetica.math.PCA
getRealEigenvalues() - Method in class umcg.genetica.math.PCA
getRefAllele() - Method in interface umcg.genetica.io.binInteraction.variant.BinaryInteractionVariant
getRefAllele() - Method in class umcg.genetica.io.binInteraction.variant.BinaryInteractionVariantAbstract
getRefAllele() - Method in class umcg.genetica.io.pileup.PileupEntry
getRegulomeDbFile() - Method in class umcg.genetica.io.regulomedb.RegulomeDbFile
getRegulomeDbScore() - Method in class umcg.genetica.io.regulomedb.RegulomeDbEntry
getReportedGenes() - Method in class umcg.genetica.io.gwascatalog.GWASTrait
getReportedGenesForCertainKey(String) - Method in class umcg.genetica.io.gwascatalog.GWASCatalog
getReverseComplement(String) - Static method in class umcg.genetica.io.trityper.util.BaseAnnot
getRight() - Method in class umcg.genetica.containers.Pair
getRight() - Method in class umcg.genetica.containers.Triple
getRiskAllele(GWASTrait) - Method in class umcg.genetica.io.gwascatalog.GWASSNP
getRiskAllele() - Method in class umcg.genetica.io.gwascatalog.GWASSNP
getRowNames() - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
getRowNameToId() - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
getRowObjects() - Method in class umcg.genetica.math.matrix2.DoubleMatrixDataset
getRowObjectsOnly(String) - Static method in class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
getRowObjectsOnly(String) - Static method in class umcg.genetica.math.matrix.DoubleMatrixDatasetRA: Deprecated.
getRsChr() - Method in class umcg.genetica.io.trityper.EQTL
getRsChrPos() - Method in class umcg.genetica.io.trityper.EQTL
getRsName() - Method in class umcg.genetica.io.trityper.EQTL
getRSquared(SNP, SNP, TriTyperGenotypeData, int, int, boolean) - Method in class umcg.genetica.io.trityper.util.DetermineLD
getrSquaredCohort() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionZscores
getSampleCount() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionCohort
getSampleCounts() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionQtlZscores
getSamplesInteractionCohort() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionZscores
getScore() - Method in class umcg.genetica.io.bed.BedEntry
getScore() - Method in class umcg.genetica.io.gtf.GffElement
getSD() - Method in class umcg.genetica.io.ucsc.UCSCTrack
getSeqname() - Method in class umcg.genetica.io.bed.BedEntry
getSeqname() - Method in class umcg.genetica.io.bedgraph.BedGraphEntry
getSeqname() - Method in class umcg.genetica.io.gtf.GffElement
getSeqname() - Method in interface umcg.genetica.variantAnnotator.GenomicRange
getSettings() - Method in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDataset
getShortestPath(int, int) - Method in class umcg.genetica.math.matrix.SymmetricByteDistanceMatrix
getShortestPath(int, int) - Method in class umcg.genetica.math.matrix.SymmetricShortDistanceMatrix
getSize() - Method in class umcg.genetica.io.fasta.LargeByteArray
getSNP(Integer) - Method in class umcg.genetica.io.trityper.TriTyperSNPMappings
getSNPId(String) - Method in class umcg.genetica.io.trityper.TriTyperSNPMappings
getSNPObject(int) - Method in class umcg.genetica.io.trityper.TriTyperGenotypeData
getSnps() - Method in class umcg.genetica.io.gwascatalog.GWASCatalog
getSNPs() - Method in class umcg.genetica.io.gwascatalog.GWASTrait
getSNPs(double) - Method in class umcg.genetica.io.gwascatalog.GWASTrait
getSnps() - Method in class umcg.genetica.io.trityper.bin.BinaryResultDataset
getSNPs() - Method in class umcg.genetica.io.trityper.TriTyperGenotypeData
getSNPs() - Method in class umcg.genetica.io.trityper.TriTyperSNPMappings
getSnpsArray() - Method in class umcg.genetica.io.gwascatalog.GWASCatalog
getSNPsForTraitContainingKey(String) - Method in class umcg.genetica.io.gwascatalog.GWASCatalog
getSnpToObj() - Method in class umcg.genetica.io.gwascatalog.GWASCatalog
getSnpToSNPId() - Method in class umcg.genetica.io.trityper.TriTyperGenotypeData
getSource() - Method in class umcg.genetica.io.gtf.GffElement
getSqrt(int) - Static method in class umcg.genetica.math.stats.Descriptives
getStart() - Method in interface umcg.genetica.collections.intervaltree.Range: Inclusive
getStart() - Method in class umcg.genetica.collections.intervaltree.StringRange
getStart() - Method in class umcg.genetica.containers.Exon
getStart() - Method in class umcg.genetica.containers.Gene
getStart() - Method in class umcg.genetica.containers.Transcript
getStart() - Method in class umcg.genetica.genomicboundaries.GenomicBoundary
getStart() - Method in class umcg.genetica.io.bed.BedEntry
getStart() - Method in class umcg.genetica.io.bedgraph.BedGraphEntry
getStart() - Method in interface umcg.genetica.io.binInteraction.gene.BinaryInteractionGene
getStart() - Method in class umcg.genetica.io.binInteraction.gene.BinaryInteractionGeneAbstract
getStart() - Method in class umcg.genetica.io.gtf.GffElement
getStart() - Method in class umcg.genetica.io.trityper.bin.BinaryResultProbe
getStop() - Method in class umcg.genetica.genomicboundaries.GenomicBoundary
getStop() - Method in class umcg.genetica.io.trityper.bin.BinaryResultProbe
getStrand() - Method in class umcg.genetica.containers.Exon
getStrand() - Method in class umcg.genetica.containers.Gene
getStrand() - Method in class umcg.genetica.containers.Transcript
getStrand() - Method in class umcg.genetica.io.gtf.GffElement
getStringToProbe() - Method in class umcg.genetica.io.trityper.bin.BinaryResultDataset
getStringToSNP() - Method in class umcg.genetica.io.trityper.bin.BinaryResultDataset
getSupportClass() - Method in class umcg.genetica.io.regulomedb.RegulomeDbSupportingData
getSupportData() - Method in class umcg.genetica.io.regulomedb.RegulomeDbEntry
getSupportMethod() - Method in class umcg.genetica.io.regulomedb.RegulomeDbSupportingData
getSupportValue() - Method in class umcg.genetica.io.regulomedb.RegulomeDbSupportingData
getTheta(int, int) - Method in class umcg.genetica.io.trityper.WGAFileMatrixRawData
getThresholdsPerRow(double[][], double[][], double, FDRUtils.CloneArrays, FDRUtils.SortArrays, FDRUtils.AbsoluteValues) - Static method in class umcg.genetica.math.stats.FDRUtils: Returns the threshold values per row in the given real data matrix that corresponds to the given false discovery rate against the null distribution from rows of given permuted data matrix.
getThresholdsPerRow(double[][], double[][][], double, FDRUtils.CloneArrays, FDRUtils.SortArrays, FDRUtils.AbsoluteValues) - Static method in class umcg.genetica.math.stats.FDRUtils: Returns the threshold values per row in the given real data matrix that corresponds to the given false discovery rate against the null distribution from rows of given permuted data matrices.
getThresholdsPerRow(double[][], String[], double, double, FDRUtils.CloneArrays, FDRUtils.SortArrays, FDRUtils.AbsoluteValues) - Static method in class umcg.genetica.math.stats.FDRUtils
getTimeDesc() - Method in class umcg.genetica.util.RunTimer
getTimeDesc(long) - Method in class umcg.genetica.util.RunTimer
getTimeDiff() - Method in class umcg.genetica.util.RunTimer
getTitle() - Method in class umcg.genetica.methylation.SoftfileAnnotation
getTopAssociations() - Method in class umcg.genetica.io.gwascatalog.GWASTrait
getTotalGGSamples() - Method in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDataset
getTotalNumberInteractions() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
getTrackInfo() - Method in class umcg.genetica.io.bed.BedFile
getTraits() - Method in class umcg.genetica.io.gwascatalog.GWASCatalog
getTraitsForCertainKey(String) - Method in class umcg.genetica.io.gwascatalog.GWASCatalog
getTraitsForCertainSnps(String) - Method in class umcg.genetica.io.gwascatalog.GWASCatalog
getTraitToObj() - Method in class umcg.genetica.io.gwascatalog.GWASCatalog
getTranscript(String) - Method in class umcg.genetica.ensembl.Features
getTranscriptHash() - Method in class umcg.genetica.ensembl.Features
getTranscripts() - Method in class umcg.genetica.containers.Gene
getTransposedDataset() - Method in class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
getType() - Method in class umcg.genetica.io.trityper.EQTL
getUseAbsoluteZScore() - Method in class umcg.genetica.io.trityper.EQTL
getValue() - Method in class umcg.genetica.collections.intervaltree.StringRange
getValue() - Method in class umcg.genetica.io.bedgraph.BedGraphEntry
getValue() - Method in class umcg.genetica.io.ucsc.UCSCDataObject
getVariant(String) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
getVariant(int) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
getVariant(String, int) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
getVariantCount() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
getVariantCount() - Method in interface umcg.genetica.io.binInteraction.gene.BinaryInteractionGene
getVariantCount() - Method in class umcg.genetica.io.binInteraction.gene.BinaryInteractionGeneCreator
getVariantCount() - Method in class umcg.genetica.io.binInteraction.gene.BinaryInteractionGeneStatic
getVariantGeneCombinations() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
getVariantId() - Method in class umcg.genetica.io.regulomedb.RegulomeDbEntry
getVariantName() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionQueryResult
getVariantPointers() - Method in interface umcg.genetica.io.binInteraction.gene.BinaryInteractionGene
getVariantPointers() - Method in class umcg.genetica.io.binInteraction.gene.BinaryInteractionGeneCreator
getVariantPointers() - Method in class umcg.genetica.io.binInteraction.gene.BinaryInteractionGeneStatic
getVariants() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
getWeightedZ(float[], int[]) - Static method in class umcg.genetica.math.stats.ZScores: Calculates a weighted Z-score according to Whitlock's paper: http://www.ncbi.nlm.nih.gov/pubmed/16135132 Square root of the sample size is used as the weight for each test.
getWeightedZ(double[], int[]) - Static method in class umcg.genetica.math.stats.ZScores: Calculates a weighted Z-score according to Whitlock's paper: http://www.ncbi.nlm.nih.gov/pubmed/16135132 Square root of the sample size is used as the weight for each test.
getWeightedZ(double[], int[], double[]) - Static method in class umcg.genetica.math.stats.ZScores: Calculates a weighted Z-score according to Whitlock's paper: http://www.ncbi.nlm.nih.gov/pubmed/16135132 Square root of the sample size is used as the weight for each test.
getWidth(String, Font) - Method in class umcg.genetica.graphics.ForestPlot
getWrittenHash() - Method in class umcg.genetica.io.bin.BinaryFile
getX(int, int, int, int) - Static method in class umcg.genetica.math.stats.ChiSquare
getX(double, double, double, double) - Static method in class umcg.genetica.math.stats.ChiSquare
getXmax() - Method in class umcg.genetica.math.interpolation.CubicSpline
getXmin() - Method in class umcg.genetica.math.interpolation.CubicSpline
getZscore() - Method in class umcg.genetica.io.trityper.EQTL
getZscoreAbs() - Method in class umcg.genetica.io.trityper.EQTL
getZscoreCovariateCohort() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionZscores
getZscoreCovariateMeta() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionZscores
getzScoreIndex() - Method in class umcg.genetica.io.trityper.bin.BinaryResultSNP
getZscoreInteractionCohort() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionZscores
getZscoreInteractionFlippedCohort() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionZscores
getZscoreInteractionFlippedMeta() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionZscores
getZscoreInteractionMeta() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionZscores
getZScorePvalueIndex(double) - Static method in class umcg.genetica.math.stats.Descriptives
getZscores() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionQtlZscores
getZscoreSnpCohort() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionZscores
getZscoreSnpMeta() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionZscores
GffAttributeFilter - Class in umcg.genetica.io.gtf
GffAttributeFilter() - Constructor for class umcg.genetica.io.gtf.GffAttributeFilter
GffElement - Class in umcg.genetica.io.gtf
GffElement(String, String, String, int, int, float, char, int, Map<String, String>) - Constructor for class umcg.genetica.io.gtf.GffElement
GffElementIterator - Class in umcg.genetica.io.gtf
GffElementIterator(GffReaderInterface) - Constructor for class umcg.genetica.io.gtf.GffElementIterator
GffReaderInterface - Interface in umcg.genetica.io.gtf
GMTFile - Class in umcg.genetica.io.gmt
GMTFile(String) - Constructor for class umcg.genetica.io.gmt.GMTFile
Goniometry - Class in umcg.genetica.math
Goniometry() - Constructor for class umcg.genetica.math.Goniometry
Gpio - Class in umcg.genetica.io
Gpio() - Constructor for class umcg.genetica.io.Gpio
gramToOunce(double) - Static method in class umcg.genetica.math.Fmath
GtfReader - Class in umcg.genetica.io.gtf
GtfReader(File) - Constructor for class umcg.genetica.io.gtf.GtfReader
GtfReader(Reader) - Constructor for class umcg.genetica.io.gtf.GtfReader
GWASCatalog - Class in umcg.genetica.io.gwascatalog
GWASCatalog() - Constructor for class umcg.genetica.io.gwascatalog.GWASCatalog
GWASCatalog(String) - Constructor for class umcg.genetica.io.gwascatalog.GWASCatalog
GWASCatalog(String, double) - Constructor for class umcg.genetica.io.gwascatalog.GWASCatalog
GWASLocus - Class in umcg.genetica.io.gwascatalog
GWASLocus() - Constructor for class umcg.genetica.io.gwascatalog.GWASLocus
GWASPublication - Class in umcg.genetica.io.gwascatalog
GWASPublication() - Constructor for class umcg.genetica.io.gwascatalog.GWASPublication
GWASSNP - Class in umcg.genetica.io.gwascatalog
GWASSNP() - Constructor for class umcg.genetica.io.gwascatalog.GWASSNP
GWASTrait - Class in umcg.genetica.io.gwascatalog
GWASTrait() - Constructor for class umcg.genetica.io.gwascatalog.GWASTrait

H

h11 - Variable in class umcg.genetica.io.trityper.util.DetermineLD
h12 - Variable in class umcg.genetica.io.trityper.util.DetermineLD
h21 - Variable in class umcg.genetica.io.trityper.util.DetermineLD
h22 - Variable in class umcg.genetica.io.trityper.util.DetermineLD
H_PLANCK - Static variable in class umcg.genetica.math.Fmath
H_PLANCK_RED - Static variable in class umcg.genetica.math.Fmath
hasAttribute(String) - Method in class umcg.genetica.io.gtf.GffElement
hasDosageInformation() - Method in class umcg.genetica.io.trityper.BufferedSNPLoader
hasDosageInformation() - Method in class umcg.genetica.io.trityper.SNP
hasDosageInformation() - Method in class umcg.genetica.io.trityper.SNPLoader
hashCode() - Method in class umcg.genetica.collections.intervaltree.StringRange
hashCode() - Method in class umcg.genetica.containers.Pair
hashCode() - Method in class umcg.genetica.containers.Triple
hashCode() - Method in class umcg.genetica.io.regulomedb.RegulomeDbEntry
hashCode() - Method in class umcg.genetica.io.regulomedb.RegulomeDbSupportingData
hashCode() - Method in class umcg.genetica.io.trityper.EQTL
hashCols - Variable in class umcg.genetica.math.matrix.DoubleMatrixDatasetAC: Deprecated.
hashCols - Variable in class umcg.genetica.math.matrix2.DoubleMatrixDataset
HashingInputStream - Class in com.mastfrog.util.streams: Wrapper for an input stream which can compute a hash as bytes are read.
HashingOutputStream - Class in com.mastfrog.util.streams: Output stream which wraps another output stream and computes a cryptographic hash using some algorithm as the data arrives.
HashingOutputStream(String, OutputStream) - Constructor for class com.mastfrog.util.streams.HashingOutputStream
hashRows - Variable in class umcg.genetica.math.matrix.DoubleMatrixDatasetAC: Deprecated.
hashRows - Variable in class umcg.genetica.math.matrix2.DoubleMatrixDataset
hashString(byte[]) - Static method in class com.mastfrog.util.streams.HashingOutputStream
hasNext() - Method in class umcg.genetica.genomicboundaries.GenomicBoundariesIterator
hasNext() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionCovariateIterator
hasNext() - Method in class umcg.genetica.io.gtf.GffElementIterator
hasNext() - Method in class umcg.genetica.io.regulomedb.RegulomeDbIterator
hasSupportDataClass(String) - Method in class umcg.genetica.io.regulomedb.RegulomeDbEntry
hav(double) - Static method in class umcg.genetica.math.Fmath
header - Static variable in class umcg.genetica.io.trityper.QTLTextFile
Heatmap - Class in umcg.genetica.graphics
Heatmap() - Constructor for class umcg.genetica.graphics.Heatmap
Heatmap.Output - Enum in umcg.genetica.graphics
Heterogeneity - Class in umcg.genetica.math.stats: This class was freely adapted from Abecasis' METAL package for meta-analysis (http://www.sph.umich.edu/csg/abecasis/Metal/)
Heterogeneity() - Constructor for class umcg.genetica.math.stats.Heterogeneity
HUGO - Static variable in class umcg.genetica.io.trityper.QTLTextFile
HUMAN_NORMAL_CHR - Static variable in class umcg.genetica.io.fasta.ReferenceGenomeFasta: CHR 1-22, X and Y
humanizeFileSize(long) - Static method in class umcg.genetica.io.Gpio
HWE - Class in umcg.genetica.math.stats
HWE() - Constructor for class umcg.genetica.math.stats.HWE
hypot(double, double) - Static method in class umcg.genetica.math.Fmath
hypot(float, float) - Static method in class umcg.genetica.math.Fmath

I

I - Static variable in class umcg.genetica.io.trityper.util.BaseAnnot
id - Variable in class umcg.genetica.containers.SortableSNP
importAnnotationFromSOFTFile(String) - Static method in class umcg.genetica.io.geofiles.ParseSoftFile
importImputedDataWithDosageInformationBeagle(String, String, String, String) - Method in class umcg.genetica.io.trityper.converters.BeagleImputedToTriTyper
importImputedDataWithDosageInformationBeagleBatches(String, String, int, String, int, int) - Method in class umcg.genetica.io.trityper.converters.BeagleImputedToTriTyper
importImputedDataWithProbabilityInformationImpute(String, String, Integer, String, String, String, String) - Method in class umcg.genetica.io.trityper.converters.ImputeImputedToTriTyperV2
importPEDFile(String[], String, int, int, int, String[], String, String, String[]) - Method in class umcg.genetica.io.trityper.converters.PedAndMapToTriTyper
importPEDFile(String, String, int, int, int, String, String, String[]) - Method in class umcg.genetica.io.trityper.converters.PedAndMapToTriTyper
importPEDFile(String, String) - Method in class umcg.genetica.io.trityper.converters.PedAndMapToTriTyper
importSOFTFile(String, int, int) - Static method in class umcg.genetica.io.geofiles.ParseSoftFile
importSOFTFileSelection(String, int, int, int) - Static method in class umcg.genetica.io.geofiles.ParseSoftFile
ImputeImputedToTriTyperV2 - Class in umcg.genetica.io.trityper.converters
ImputeImputedToTriTyperV2() - Constructor for class umcg.genetica.io.trityper.converters.ImputeImputedToTriTyperV2
in - Variable in class umcg.genetica.io.text.TextFile
inchToMillimetre(double) - Static method in class umcg.genetica.math.Fmath
INCLUDE_CASES - Static variable in class umcg.genetica.io.trityper.util.DetermineLD
INCLUDE_CASES_AND_CONTROLS - Static variable in class umcg.genetica.io.trityper.util.DetermineLD
INCLUDE_CONTROLS - Static variable in class umcg.genetica.io.trityper.util.DetermineLD
Independifier - Class in umcg.genetica.gwas: All shall be independent.
Independifier(String) - Constructor for class umcg.genetica.gwas.Independifier
Independifier(TriTyperGenotypeData, SNPLoader) - Constructor for class umcg.genetica.gwas.Independifier
independify(String[], double, int) - Method in class umcg.genetica.gwas.Independifier: Independifies given SNPs with given thresholds.
independify(String, int, double, double, int, int) - Method in class umcg.genetica.gwas.Independifier
independify(String, int, double, double, int, int, String) - Method in class umcg.genetica.gwas.Independifier
indexOf(double[], double) - Static method in class umcg.genetica.math.Fmath
indexOf(float[], float) - Static method in class umcg.genetica.math.Fmath
indexOf(long[], long) - Static method in class umcg.genetica.math.Fmath
indexOf(int[], int) - Static method in class umcg.genetica.math.Fmath
indexOf(byte[], byte) - Static method in class umcg.genetica.math.Fmath
indexOf(short[], short) - Static method in class umcg.genetica.math.Fmath
indexOf(char[], char) - Static method in class umcg.genetica.math.Fmath
indexOf(String[], String) - Static method in class umcg.genetica.math.Fmath
indexOf(Object[], Object) - Static method in class umcg.genetica.math.Fmath
indicesOf(double[], double) - Static method in class umcg.genetica.math.Fmath
indicesOf(float[], float) - Static method in class umcg.genetica.math.Fmath
indicesOf(long[], long) - Static method in class umcg.genetica.math.Fmath
indicesOf(int[], int) - Static method in class umcg.genetica.math.Fmath
indicesOf(short[], short) - Static method in class umcg.genetica.math.Fmath
indicesOf(byte[], byte) - Static method in class umcg.genetica.math.Fmath
indicesOf(char[], char) - Static method in class umcg.genetica.math.Fmath
indicesOf(String[], String) - Static method in class umcg.genetica.math.Fmath
indicesOf(Object[], Object) - Static method in class umcg.genetica.math.Fmath
initializeZScoreToPValue() - Static method in class umcg.genetica.math.stats.Descriptives
InplaceArrayQuickSort - Class in umcg.genetica.util
InplaceArrayQuickSort() - Constructor for class umcg.genetica.util.InplaceArrayQuickSort
interpolate(double) - Method in class umcg.genetica.math.interpolation.CubicSpline
interpolate(double, double[], double[], double[]) - Static method in class umcg.genetica.math.interpolation.CubicSpline
interpolate_for_y_and_dydx(double) - Method in class umcg.genetica.math.interpolation.CubicSpline
IntervalTree<E extends Range> - Class in umcg.genetica.collections.intervaltree
IntervalTree(E[], Class<E>) - Constructor for class umcg.genetica.collections.intervaltree.IntervalTree
IntervalTree(List<E>, Class<E>) - Constructor for class umcg.genetica.collections.intervaltree.IntervalTree
intTOdouble(int[]) - Static method in class umcg.genetica.math.Fmath
intTOfloat(int[]) - Static method in class umcg.genetica.math.Fmath
intTOlong(int[]) - Static method in class umcg.genetica.math.Fmath
intValue - Variable in class umcg.genetica.containers.StringIntegerObject
InversionCallsToTriTyper - Class in umcg.genetica.io.trityper.converters
InversionCallsToTriTyper() - Constructor for class umcg.genetica.io.trityper.converters.InversionCallsToTriTyper
invertElements(double[]) - Static method in class umcg.genetica.math.Fmath
invertElements(float[]) - Static method in class umcg.genetica.math.Fmath
is - Variable in class umcg.genetica.io.bin.BinaryFile
isChromosomeInBoundary(String) - Method in class umcg.genetica.genomicboundaries.GenomicBoundaries: Method to check if a chromosome is contained in the Genomic Boundaries.
isChromosomeInBoundary(String) - Method in class umcg.genetica.genomicboundaries.GenomicBoundariesSimple
isDir(String) - Static method in class umcg.genetica.io.Gpio
isEmpty() - Method in class umcg.genetica.collections.intervaltree.IntervalTree
isEqual(double, double) - Static method in class umcg.genetica.math.Fmath
isEqual(float, float) - Static method in class umcg.genetica.math.Fmath
isEqual(int, int) - Static method in class umcg.genetica.math.Fmath
isEqual(char, char) - Static method in class umcg.genetica.math.Fmath
isEqual(String, String) - Static method in class umcg.genetica.math.Fmath
isEqualWithinLimits(double, double, double) - Static method in class umcg.genetica.math.Fmath
isEqualWithinLimits(float, float, float) - Static method in class umcg.genetica.math.Fmath
isEqualWithinLimits(long, long, long) - Static method in class umcg.genetica.math.Fmath
isEqualWithinLimits(int, int, int) - Static method in class umcg.genetica.math.Fmath
isEqualWithinLimits(BigDecimal, BigDecimal, BigDecimal) - Static method in class umcg.genetica.math.Fmath
isEqualWithinLimits(BigInteger, BigInteger, BigInteger) - Static method in class umcg.genetica.math.Fmath
isEqualWithinPerCent(double, double, double) - Static method in class umcg.genetica.math.Fmath
isEqualWithinPerCent(float, float, float) - Static method in class umcg.genetica.math.Fmath
isEqualWithinPerCent(long, long, double) - Static method in class umcg.genetica.math.Fmath
isEqualWithinPerCent(long, long, long) - Static method in class umcg.genetica.math.Fmath
isEqualWithinPerCent(int, int, double) - Static method in class umcg.genetica.math.Fmath
isEqualWithinPerCent(int, int, int) - Static method in class umcg.genetica.math.Fmath
isEqualWithinPerCent(BigDecimal, BigDecimal, BigDecimal) - Static method in class umcg.genetica.math.Fmath
isEqualWithinPerCent(BigInteger, BigInteger, BigDecimal) - Static method in class umcg.genetica.math.Fmath
isEqualWithinPerCent(BigInteger, BigInteger, BigInteger) - Static method in class umcg.genetica.math.Fmath
isEven(int) - Static method in class umcg.genetica.math.Fmath
isEven(float) - Static method in class umcg.genetica.math.Fmath
isEven(double) - Static method in class umcg.genetica.math.Fmath
isExpressionDataLoadedCorrectly() - Method in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDataset
isFlippedZscoreStored() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
isInBoundarie(int) - Method in class umcg.genetica.genomicboundaries.GenomicBoundary: Assumes that chromosome is correct
isInBoundarie(int, int) - Method in class umcg.genetica.genomicboundaries.GenomicBoundary: Assumes that chromosome is correct
isInBoundary(String, int, int) - Method in class umcg.genetica.genomicboundaries.GenomicBoundaries
isInBoundary(String, int) - Method in class umcg.genetica.genomicboundaries.GenomicBoundariesSimple
isInfinity(double) - Static method in class umcg.genetica.math.Fmath
isInfinity(float) - Static method in class umcg.genetica.math.Fmath
isInteger(double) - Static method in class umcg.genetica.math.Fmath
isInteger(double[]) - Static method in class umcg.genetica.math.Fmath
isInteger(float) - Static method in class umcg.genetica.math.Fmath
isInteger(float[]) - Static method in class umcg.genetica.math.Fmath
isInteger(Number) - Static method in class umcg.genetica.math.Fmath
isInteger(Number[]) - Static method in class umcg.genetica.math.Fmath
isMetaAnalysis() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
isMinusInfinity(double) - Static method in class umcg.genetica.math.Fmath
isMinusInfinity(float) - Static method in class umcg.genetica.math.Fmath
isNaN(double) - Static method in class umcg.genetica.math.Fmath
isNaN(float) - Static method in class umcg.genetica.math.Fmath
isNormalQtlStored() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
isNumeric(String) - Static method in class umcg.genetica.io.geofiles.ParseTextTable
isOdd(int) - Static method in class umcg.genetica.math.Fmath
isOdd(float) - Static method in class umcg.genetica.math.Fmath
isOdd(double) - Static method in class umcg.genetica.math.Fmath
isOverlaping(GenomicBoundary) - Method in class umcg.genetica.genomicboundaries.GenomicBoundary
isPartOfBoundary(GenomicBoundary) - Method in class umcg.genetica.genomicboundaries.GenomicBoundary: Is this boundary a sub boundary of the other boundary.
isPlusInfinity(double) - Static method in class umcg.genetica.math.Fmath
isPlusInfinity(float) - Static method in class umcg.genetica.math.Fmath
isReadOnly() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
isTopAssociation(GWASSNP) - Method in class umcg.genetica.io.gwascatalog.GWASTrait
iterate() - Method in class umcg.genetica.console.ProgressBar
iterator() - Method in class umcg.genetica.collections.ChrPosMap
iterator() - Method in class umcg.genetica.collections.ChrPosTreeMap
iterator() - Method in class umcg.genetica.genomicboundaries.GenomicBoundaries
iterator() - Method in class umcg.genetica.io.bed.BedFile
iterator() - Method in class umcg.genetica.io.bedgraph.BedGraphFile
iterator() - Method in class umcg.genetica.io.gtf.GtfReader
iterator() - Method in class umcg.genetica.io.pileup.PileupFile
iterator() - Method in class umcg.genetica.io.regulomedb.RegulomeDbFile
iterator() - Method in class umcg.genetica.io.regulomedb.RegulomeDbFiles
iterator() - Method in class umcg.genetica.io.text.TextFile

J

jouleToCalorie(double) - Static method in class umcg.genetica.math.Fmath

K

K_BOLTZMANN - Static variable in class umcg.genetica.math.Fmath
kelvinToCelsius(double) - Static method in class umcg.genetica.math.Fmath
kgToPound(double) - Static method in class umcg.genetica.math.Fmath
kgToTon(double) - Static method in class umcg.genetica.math.Fmath
kmPerLitreToMilePerGallon(double) - Static method in class umcg.genetica.math.Fmath
kmToMile(double) - Static method in class umcg.genetica.math.Fmath
KolmogorovSmirnov - Class in umcg.genetica.math.stats
KolmogorovSmirnov() - Constructor for class umcg.genetica.math.stats.KolmogorovSmirnov

L

LargeByteArray - Class in umcg.genetica.io.fasta
LargeByteArray(long) - Constructor for class umcg.genetica.io.fasta.LargeByteArray
leapYear(int) - Static method in class umcg.genetica.math.Fmath
length() - Method in class umcg.genetica.io.bin.RandomAccessFile: Get the length of the file.
LINE - Static variable in class umcg.genetica.console.ConsoleGUIElems
litrePerKmToGallonPerMile(double) - Static method in class umcg.genetica.math.Fmath
litreToGallon(double) - Static method in class umcg.genetica.math.Fmath
litreToPint(double) - Static method in class umcg.genetica.math.Fmath
litreToQuart(double) - Static method in class umcg.genetica.math.Fmath
lnElements(double[]) - Static method in class umcg.genetica.math.Fmath
lnElements(float[]) - Static method in class umcg.genetica.math.Fmath
load(File) - Static method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
load(File, boolean) - Static method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
load(String) - Method in class umcg.genetica.io.trityper.ProbeAnnotation
load(String) - Method in class umcg.genetica.io.trityper.probeannotation.ProbeTranslation
load(String, String, String, boolean) - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
load(String) - Method in class umcg.genetica.io.trityper.TriTyperGenotypeData
load(File) - Method in class umcg.genetica.math.matrix.SymmetricByteDistanceMatrix
load(File) - Method in class umcg.genetica.math.matrix.SymmetricShortDistanceMatrix
loadAnnotation(String) - Method in class umcg.genetica.ensembl.Features
loadDosage(SNP) - Method in class umcg.genetica.io.trityper.BufferedSNPLoader
loadDosage(SNP) - Method in class umcg.genetica.io.trityper.SNPLoader
loadDoubleData(String) - Static method in class umcg.genetica.math.matrix2.DoubleMatrixDataset
loadDoubleTextData(String, String) - Static method in class umcg.genetica.math.matrix2.DoubleMatrixDataset
loadedChr(String) - Method in class umcg.genetica.io.fasta.ReferenceGenomeFasta
loadExpressionData(String, String, int) - Method in class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
loadFamFile(String) - Method in class umcg.genetica.io.trityper.converters.BeagleImputedToTriTyper
loadGenotypes(SNP) - Method in class umcg.genetica.io.trityper.BufferedSNPLoader
loadGenotypes(SNP) - Method in class umcg.genetica.io.trityper.SNPLoader
loadSubsetOfTextDoubleData(String, String, HashSet<String>, HashSet<String>) - Static method in class umcg.genetica.math.matrix2.DoubleMatrixDataset
loadSuccess - Variable in class umcg.genetica.math.matrix.SymmetricByteDistanceMatrix
loc - Variable in class umcg.genetica.io.bin.BinaryFile
log(double) - Static method in class umcg.genetica.math.Fmath
log(float) - Static method in class umcg.genetica.math.Fmath
log10(double) - Static method in class umcg.genetica.math.Fmath
log10(float) - Static method in class umcg.genetica.math.Fmath
log10(double, double) - Static method in class umcg.genetica.math.Fmath
log10(double, int) - Static method in class umcg.genetica.math.Fmath
log10(float, float) - Static method in class umcg.genetica.math.Fmath
log10(float, int) - Static method in class umcg.genetica.math.Fmath
log10Elements(double[]) - Static method in class umcg.genetica.math.Fmath
log10Elements(float[]) - Static method in class umcg.genetica.math.Fmath
log2(double) - Static method in class umcg.genetica.math.Fmath
log2(float) - Static method in class umcg.genetica.math.Fmath
Log2Transform - Class in umcg.genetica.math.stats
Log2Transform() - Constructor for class umcg.genetica.math.stats.Log2Transform
log2transform(double[][]) - Static method in class umcg.genetica.math.stats.Log2Transform
logFactorial(int) - Static method in class umcg.genetica.math.Fmath
logFactorial(long) - Static method in class umcg.genetica.math.Fmath
logFactorial(double) - Static method in class umcg.genetica.math.Fmath
logtransform - Variable in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDatasetSettings
longTOdouble(long[]) - Static method in class umcg.genetica.math.Fmath
longTOfloat(long[]) - Static method in class umcg.genetica.math.Fmath
lookupSqrt(int) - Static method in class umcg.genetica.math.stats.Descriptives
lt(Object, Object) - Method in class umcg.genetica.util.StringDoubleObjectSorterSortOnDouble: Override object comparer
lt(Object, Object) - Method in class umcg.genetica.util.StringIntegerObjectSorterSortOnInteger: Override object comparer
lt(Object, Object) - Method in class umcg.genetica.util.VectorSorter: Compare two objects.

M

m_correlationToZScore - Static variable in class umcg.genetica.math.stats.Correlation
M_ELECTRON - Static variable in class umcg.genetica.math.Fmath
M_NEUTRON - Static variable in class umcg.genetica.math.Fmath
M_PROTON - Static variable in class umcg.genetica.math.Fmath
m_sqrtSample - Static variable in class umcg.genetica.math.stats.Descriptives
m_zScoreToPValue - Static variable in class umcg.genetica.math.stats.Descriptives
MachImputedToTriTyper - Class in umcg.genetica.io.trityper.converters
MachImputedToTriTyper(String, String) - Constructor for class umcg.genetica.io.trityper.converters.MachImputedToTriTyper
MachImputedTransposedDosageToTriTyper - Class in umcg.genetica.io.trityper.converters
MachImputedTransposedDosageToTriTyper(String, String, String) - Constructor for class umcg.genetica.io.trityper.converters.MachImputedTransposedDosageToTriTyper
MAGIC_1 - Static variable in class umcg.genetica.io.binInteraction.BinaryInteractionFile
MAGIC_2 - Static variable in class umcg.genetica.io.binInteraction.BinaryInteractionFile
main(String[]) - Static method in class umcg.genetica.io.gtf.TestGffIntervalTree
main(String[]) - Static method in class umcg.genetica.io.pileup.PileupToVcf
main(String[]) - Static method in class umcg.genetica.io.trityper.ConvertDoubleMatrixDataToTriTyper
main(String[]) - Static method in class umcg.genetica.io.trityper.converters.FinalReportToTriTyper
main(String[]) - Static method in class umcg.genetica.io.trityper.converters.TriTyperToMachImputedTransposed
main(String[]) - Static method in class umcg.genetica.io.trityper.util.TriTyperGenotypeDataMerger
main(String[]) - Static method in class umcg.genetica.math.stats.TheilSen
main(String[]) - Static method in class umcg.genetica.methylation.AssociatingPcasWithAnnotation
main(String[]) - Static method in class umcg.genetica.methylation.MethylationAssociatoingAnnotationWithValues
main(String[]) - Static method in class umcg.genetica.text.parsing.Demographics
main(String[]) - Static method in class umcg.genetica.util.CheckAssocationMultipleGeneProbes
mark(int) - Method in class com.mastfrog.util.streams.HashingInputStream
markSupported() - Method in class com.mastfrog.util.streams.HashingInputStream
matrix - Variable in class umcg.genetica.math.matrix2.DoubleMatrixDataset
MatrixHandling - Class in umcg.genetica.math.matrix
MatrixHandling() - Constructor for class umcg.genetica.math.matrix.MatrixHandling
MatrixHandling - Class in umcg.genetica.math.matrix2
MatrixHandling() - Constructor for class umcg.genetica.math.matrix2.MatrixHandling
MatrixTools - Class in umcg.genetica.math.matrix
MatrixTools() - Constructor for class umcg.genetica.math.matrix.MatrixTools
MatrixTools - Class in umcg.genetica.math.matrix2
MatrixTools() - Constructor for class umcg.genetica.math.matrix2.MatrixTools
max(double[]) - Static method in class umcg.genetica.util.Primitives
max(double[][]) - Static method in class umcg.genetica.util.Primitives
max(char[]) - Static method in class umcg.genetica.util.Primitives
max(byte[]) - Static method in class umcg.genetica.util.Primitives
max(short[]) - Static method in class umcg.genetica.util.Primitives
max(int[]) - Static method in class umcg.genetica.util.Primitives
max(long[]) - Static method in class umcg.genetica.util.Primitives
MAX_VALUE - Static variable in class umcg.genetica.math.matrix.SymmetricByteDistanceMatrix
MAX_VALUE - Static variable in class umcg.genetica.math.matrix.SymmetricShortDistanceMatrix
maxByte(byte...) - Static method in class umcg.genetica.util.Primitives
maxChar(char...) - Static method in class umcg.genetica.util.Primitives
maxDouble(double...) - Static method in class umcg.genetica.util.Primitives
maximum(double[]) - Static method in class umcg.genetica.math.Fmath
maximum(float[]) - Static method in class umcg.genetica.math.Fmath
maximum(int[]) - Static method in class umcg.genetica.math.Fmath
maximum(long[]) - Static method in class umcg.genetica.math.Fmath
maximumDifference(double[]) - Static method in class umcg.genetica.math.Fmath
maximumDifference(float[]) - Static method in class umcg.genetica.math.Fmath
maximumDifference(long[]) - Static method in class umcg.genetica.math.Fmath
maximumDifference(int[]) - Static method in class umcg.genetica.math.Fmath
maxInt(int...) - Static method in class umcg.genetica.util.Primitives
maxLong(long...) - Static method in class umcg.genetica.util.Primitives
maxShort(short...) - Static method in class umcg.genetica.util.Primitives
maxValue() - Method in class umcg.genetica.math.matrix.SymmetricByteDistanceMatrix
maxValue() - Method in class umcg.genetica.math.matrix.SymmetricShortDistanceMatrix
mean(float[]) - Static method in class umcg.genetica.math.stats.Descriptives: Calculate the mean for an array of floats
mean(double[]) - Static method in class umcg.genetica.math.stats.Descriptives
mean(double[], double[]) - Static method in class umcg.genetica.math.stats.Descriptives: Simultainiusly calculates mean for two double[] of the same lengths Warning: Does not check if the lenght is identical!
mergeDatasetsOnCommonSamples(String[], String) - Method in class umcg.genetica.io.trityper.util.TriTyperGenotypeDataMerger
MergeDoubleMatrices - Class in umcg.genetica.math.matrix
MergeDoubleMatrices() - Constructor for class umcg.genetica.math.matrix.MergeDoubleMatrices
MergeDoubleMatrices - Class in umcg.genetica.math.matrix2
MergeDoubleMatrices() - Constructor for class umcg.genetica.math.matrix2.MergeDoubleMatrices
mergeGenomicBoundaries(GenomicBoundaries) - Method in class umcg.genetica.genomicboundaries.GenomicBoundaries: Merges GenomicBoundaries by adding
mergeMatrixBasedOnColumns(DoubleMatrixDataset<String, String>, DoubleMatrixDataset<String, String>, boolean) - Static method in class umcg.genetica.math.matrix.MergeDoubleMatrices: Merge a matrix based on shared column identifiers.
mergeMatrixBasedOnColumns(DoubleMatrixDataset<String, String>, DoubleMatrixDataset<String, String>, boolean) - Static method in class umcg.genetica.math.matrix2.MergeDoubleMatrices: Merge a matrix based on shared column identifiers.
mergeMatrixBasedOnRows(DoubleMatrixDataset<String, String>, DoubleMatrixDataset<String, String>, boolean) - Static method in class umcg.genetica.math.matrix.MergeDoubleMatrices: Merge a matrix based on row identifiers.
mergeMatrixBasedOnRows(DoubleMatrixDataset<String, String>, DoubleMatrixDataset<String, String>, boolean) - Static method in class umcg.genetica.math.matrix2.MergeDoubleMatrices: Merge a matrix based on row identifiers.
mergeOverlappingBoundaries() - Method in class umcg.genetica.genomicboundaries.GenomicBoundaries: Method that merges overlapping Boundaries.
METAB - Static variable in class umcg.genetica.io.trityper.QTLTextFile
METAZ - Static variable in class umcg.genetica.io.trityper.QTLTextFile
MethylationAssociatoingAnnotationWithValues - Class in umcg.genetica.methylation
MethylationAssociatoingAnnotationWithValues() - Constructor for class umcg.genetica.methylation.MethylationAssociatoingAnnotationWithValues
metreToFoot(double) - Static method in class umcg.genetica.math.Fmath
metreToYard(double) - Static method in class umcg.genetica.math.Fmath
milePerGallonToKmPerLitre(double) - Static method in class umcg.genetica.math.Fmath
mileToKm(double) - Static method in class umcg.genetica.math.Fmath
millimetreToInch(double) - Static method in class umcg.genetica.math.Fmath
min(double[]) - Static method in class umcg.genetica.util.Primitives
min(double[][]) - Static method in class umcg.genetica.util.Primitives
min(char[]) - Static method in class umcg.genetica.util.Primitives
min(byte[]) - Static method in class umcg.genetica.util.Primitives
min(short[]) - Static method in class umcg.genetica.util.Primitives
min(int[]) - Static method in class umcg.genetica.util.Primitives
min(long[]) - Static method in class umcg.genetica.util.Primitives
minByte(byte...) - Static method in class umcg.genetica.util.Primitives
minChar(char...) - Static method in class umcg.genetica.util.Primitives
minDouble(double...) - Static method in class umcg.genetica.util.Primitives
MinimacImputedToTriTyper - Class in umcg.genetica.io.trityper.converters
MinimacImputedToTriTyper() - Constructor for class umcg.genetica.io.trityper.converters.MinimacImputedToTriTyper
minimum(double[]) - Static method in class umcg.genetica.math.Fmath
minimum(float[]) - Static method in class umcg.genetica.math.Fmath
minimum(int[]) - Static method in class umcg.genetica.math.Fmath
minimum(long[]) - Static method in class umcg.genetica.math.Fmath
minimumDifference(double[]) - Static method in class umcg.genetica.math.Fmath
minimumDifference(float[]) - Static method in class umcg.genetica.math.Fmath
minimumDifference(long[]) - Static method in class umcg.genetica.math.Fmath
minimumDifference(int[]) - Static method in class umcg.genetica.math.Fmath
minInt(int...) - Static method in class umcg.genetica.util.Primitives
minLong(long...) - Static method in class umcg.genetica.util.Primitives
minShort(short...) - Static method in class umcg.genetica.util.Primitives
mode - Variable in class umcg.genetica.io.bin.RandomAccessFile: The access mode of the file.
molarToPercentWeightByVol(double, double) - Static method in class umcg.genetica.math.Fmath
moveFile(String, String) - Static method in class umcg.genetica.io.Gpio
MU_0 - Static variable in class umcg.genetica.math.Fmath
MultiThreadedInPlaceQuickSort - Class in umcg.genetica.util
MultiThreadedInPlaceQuickSort() - Constructor for class umcg.genetica.util.MultiThreadedInPlaceQuickSort
Mvalue(DoubleMatrixDataset<String, String>, DoubleMatrixDataset<String, String>) - Static method in class umcg.genetica.methylation.ConverteUandMTo

N

N - Static variable in class umcg.genetica.io.trityper.util.BaseAnnot
N_AVAGADRO - Static variable in class umcg.genetica.math.Fmath
name - Variable in class umcg.genetica.containers.SortableSNP
name - Variable in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDatasetSettings
nearestElementIndex(double[], double) - Static method in class umcg.genetica.math.Fmath
nearestElementIndex(int[], int) - Static method in class umcg.genetica.math.Fmath
nearestElementValue(double[], double) - Static method in class umcg.genetica.math.Fmath
nearestElementValue(int[], int) - Static method in class umcg.genetica.math.Fmath
nearestHigherElementIndex(double[], double) - Static method in class umcg.genetica.math.Fmath
nearestHigherElementIndex(int[], int) - Static method in class umcg.genetica.math.Fmath
nearestHigherElementValue(double[], double) - Static method in class umcg.genetica.math.Fmath
nearestHigherElementValue(int[], int) - Static method in class umcg.genetica.math.Fmath
nearestLowerElementIndex(double[], double) - Static method in class umcg.genetica.math.Fmath
nearestLowerElementIndex(int[], int) - Static method in class umcg.genetica.math.Fmath
nearestLowerElementValue(double[], double) - Static method in class umcg.genetica.math.Fmath
nearestLowerElementValue(int[], int) - Static method in class umcg.genetica.math.Fmath
NetworkConverter - Class in umcg.genetica.io.text.converters
next() - Method in class umcg.genetica.genomicboundaries.GenomicBoundariesIterator
next() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionCovariateIterator
next() - Method in class umcg.genetica.io.gtf.GffElementIterator
next() - Method in class umcg.genetica.io.regulomedb.RegulomeDbIterator
nextElement() - Method in interface umcg.genetica.io.gtf.GffReaderInterface
nextElement() - Method in class umcg.genetica.io.gtf.GtfReader
nmToEv(double) - Static method in class umcg.genetica.math.Fmath
Normalization - Class in umcg.genetica.math.stats
noRoundingErrorCheck() - Static method in class umcg.genetica.math.interpolation.CubicSpline
nrCalled - Variable in class umcg.genetica.io.trityper.SNP
nrCalledGenotypes - Variable in class umcg.genetica.io.trityper.util.DetermineLD
nrCols - Variable in class umcg.genetica.math.matrix.DoubleMatrixDatasetAC: Deprecated.
nrColsTotal - Variable in class umcg.genetica.math.matrix.DoubleMatrixDatasetRA: Deprecated.
nrInds - Variable in class umcg.genetica.io.trityper.WGAFileMatrixGenotype
nrInds - Variable in class umcg.genetica.io.trityper.WGAFileMatrixImputedDosage
nrInds - Variable in class umcg.genetica.io.trityper.WGAFileMatrixRawData
nrRows - Variable in class umcg.genetica.math.matrix.DoubleMatrixDatasetAC: Deprecated.
nrSNPs - Variable in class umcg.genetica.io.trityper.WGAFileMatrixGenotype
nrSNPs - Variable in class umcg.genetica.io.trityper.WGAFileMatrixImputedDosage
nrSNPs - Variable in class umcg.genetica.io.trityper.WGAFileMatrixRawData
nsinc(double) - Static method in class umcg.genetica.math.Fmath

O

oneDarray(int, int) - Static method in class umcg.genetica.math.interpolation.CubicSpline
open() - Method in class umcg.genetica.io.text.TextFile
openMatrix(int) - Method in class umcg.genetica.io.trityper.bin.BinaryResultDataset
OrderOnColumnnames() - Method in class umcg.genetica.math.matrix2.DoubleMatrixDataset: Order columns
OrderOnColumns(DoubleMatrixDataset) - Static method in class umcg.genetica.math.matrix.MatrixHandling: Order columns
OrderOnRownames() - Method in class umcg.genetica.math.matrix2.DoubleMatrixDataset: Order rows
OrderOnRows(DoubleMatrixDataset) - Static method in class umcg.genetica.math.matrix.MatrixHandling: Order rows
orderPoints() - Method in class umcg.genetica.math.interpolation.CubicSpline
os - Variable in class umcg.genetica.io.bin.BinaryFile
ounceToGram(double) - Static method in class umcg.genetica.math.Fmath
out - Variable in class umcg.genetica.io.text.TextFile
outputDosageInformation(String, String, String, boolean) - Method in class umcg.genetica.io.trityper.converters.TriTyperToPlinkDosage

P

Pair<L,R> - Class in umcg.genetica.containers
Pair(L, R) - Constructor for class umcg.genetica.containers.Pair
Pair(L, R, Pair.SORTBY) - Constructor for class umcg.genetica.containers.Pair
Pair(L, R, String) - Constructor for class umcg.genetica.containers.Pair
Pair(L, R, String, Pair.SORTBY) - Constructor for class umcg.genetica.containers.Pair
Pair.SORTBY - Enum in umcg.genetica.containers
pairwiseCorrelation(double[][]) - Method in class umcg.genetica.math.stats.concurrent.ConcurrentCorrelation
pairwiseCorrelationDoubleMatrix(double[][]) - Method in class umcg.genetica.math.stats.concurrent.ConcurrentCorrelation
pairwiseCovariation(double[][]) - Method in class umcg.genetica.math.stats.concurrent.ConcurrentCovariation
pairwiseCovariationDoubleMatrix(double[][]) - Method in class umcg.genetica.math.stats.concurrent.ConcurrentCovariation
parse(String, String) - Method in class umcg.genetica.io.trityper.converters.VCFToTriTyper: Parse and assume all variants are SNPs
parse(String, String, String) - Method in class umcg.genetica.io.trityper.converters.VCFToTriTyper: Parser that can filter variants to only include SNPs
parseByte(byte) - Static method in class umcg.genetica.io.trityper.util.ChrAnnotation
parseChr(String) - Static method in class umcg.genetica.io.trityper.util.ChrAnnotation
parseGeoTables(String, boolean) - Static method in class umcg.genetica.io.geofiles.ParseTextTable: Geo text tables for HT12 v3 / v4 data
parseLn() - Method in class umcg.genetica.io.ucsc.PeakFile
parseLn() - Method in class umcg.genetica.io.ucsc.WigFile
parsePileupLine(String, int) - Static method in class umcg.genetica.io.pileup.PileupFile
ParseSoftFile - Class in umcg.genetica.io.geofiles
ParseSoftFile() - Constructor for class umcg.genetica.io.geofiles.ParseSoftFile
parseTCGAData450As27K_lvl1(String, boolean, String, boolean, HashMap<String, Boolean>) - Static method in class umcg.genetica.methylation.ParseTcgaMethylationFile: Read Level 1 450K data from TGCA a single DoubleMatrixDatasets containing beta values.
parseTCGAData_lvl1(String, boolean, String, boolean) - Static method in class umcg.genetica.methylation.ParseTcgaMethylationFile: Read Level 1 data from TGCA a single DoubleMatrixDatasets containing beta values.
parseTCGAData_lvl1_all_matrices(String, boolean, String, boolean) - Static method in class umcg.genetica.methylation.ParseTcgaMethylationFile: Read Level 1 data from TGCA Return 3 DoubleMatrixDatasets, methylated probe values, un-methylated probe values and beta values.
parseTCGAData_lvl3(String, int, boolean, String) - Static method in class umcg.genetica.methylation.ParseTcgaMethylationFile: Read level 3 data from TCGA Return DoubleMatrixDataset beta-values
ParseTcgaMethylationFile - Class in umcg.genetica.methylation
ParseTcgaMethylationFile() - Constructor for class umcg.genetica.methylation.ParseTcgaMethylationFile
ParseTextTable - Class in umcg.genetica.io.geofiles
ParseTextTable() - Constructor for class umcg.genetica.io.geofiles.ParseTextTable
passesQC() - Method in class umcg.genetica.io.trityper.SNP
PCA - Class in umcg.genetica.math
PCA() - Constructor for class umcg.genetica.math.PCA
PCA() - Method in class umcg.genetica.math.PCA
PeakFile - Class in umcg.genetica.io.ucsc
PeakFile(String, boolean) - Constructor for class umcg.genetica.io.ucsc.PeakFile
PeakFile(String, boolean, PeakFile.PEAKFORMAT) - Constructor for class umcg.genetica.io.ucsc.PeakFile
PeakFile.PEAKFORMAT - Enum in umcg.genetica.io.ucsc
PedAndMapToTriTyper - Class in umcg.genetica.io.trityper.converters
PedAndMapToTriTyper() - Constructor for class umcg.genetica.io.trityper.converters.PedAndMapToTriTyper
percentWeightByVolToMolar(double, double) - Static method in class umcg.genetica.math.Fmath
PerChrIntervalTree<E extends Range> - Class in umcg.genetica.collections.intervaltree
PerChrIntervalTree(Class<E>) - Constructor for class umcg.genetica.collections.intervaltree.PerChrIntervalTree
performQC(DoubleMatrixDataset<String, String>, ArrayList<String>, ArrayList<String>, boolean, int, int) - Static method in class umcg.genetica.math.matrix.MatrixHandling: Method to apply all QC steps.
permuteCovariates(Random) - Method in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDataset
permuteSampleLables(Random) - Method in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDataset: Permutes the mapping between genotype and gene expression samples
PI - Static variable in class umcg.genetica.math.Fmath
PileupEntry - Class in umcg.genetica.io.pileup
PileupEntry(String, int, Allele, int, String, int) - Constructor for class umcg.genetica.io.pileup.PileupEntry: Only handles SNPs
PileupEntry(String, int, Allele, int, String, String, int) - Constructor for class umcg.genetica.io.pileup.PileupEntry
PileupFile - Class in umcg.genetica.io.pileup
PileupFile(String, int) - Constructor for class umcg.genetica.io.pileup.PileupFile
PileupFile(File, int) - Constructor for class umcg.genetica.io.pileup.PileupFile
PileupParseException - Exception in umcg.genetica.io.pileup
PileupParseException() - Constructor for exception umcg.genetica.io.pileup.PileupParseException: Creates a new instance of PileupParseException without detail message.
PileupParseException(String) - Constructor for exception umcg.genetica.io.pileup.PileupParseException: Constructs an instance of PileupParseException with the specified detail message.
PileupToVcf - Class in umcg.genetica.io.pileup
PileupToVcf() - Constructor for class umcg.genetica.io.pileup.PileupToVcf
pintToLitre(double) - Static method in class umcg.genetica.math.Fmath
pintUKtoCupUS(double) - Static method in class umcg.genetica.math.Fmath
pintUKtoUS(double) - Static method in class umcg.genetica.math.Fmath
pintUStoUK(double) - Static method in class umcg.genetica.math.Fmath
pipe - Static variable in class umcg.genetica.text.Strings
plot(double, double, double, String, String) - Method in class umcg.genetica.graphics.VennDiagram
potentialRoundingError(double) - Static method in class umcg.genetica.math.interpolation.CubicSpline
poundToKg(double) - Static method in class umcg.genetica.math.Fmath
Primitives - Class in umcg.genetica.util
Primitives() - Constructor for class umcg.genetica.util.Primitives
print() - Method in class umcg.genetica.console.ProgressBar
print(double[]) - Static method in class umcg.genetica.math.Fmath
print(float[]) - Static method in class umcg.genetica.math.Fmath
print(int[]) - Static method in class umcg.genetica.math.Fmath
print(long[]) - Static method in class umcg.genetica.math.Fmath
print(char[]) - Static method in class umcg.genetica.math.Fmath
print(String[]) - Static method in class umcg.genetica.math.Fmath
print(short[]) - Static method in class umcg.genetica.math.Fmath
print(byte[]) - Static method in class umcg.genetica.math.Fmath
print(double[][]) - Static method in class umcg.genetica.math.Fmath
println(double[]) - Static method in class umcg.genetica.math.Fmath
println(float[]) - Static method in class umcg.genetica.math.Fmath
println(int[]) - Static method in class umcg.genetica.math.Fmath
println(long[]) - Static method in class umcg.genetica.math.Fmath
println(char[]) - Static method in class umcg.genetica.math.Fmath
println(String[]) - Static method in class umcg.genetica.math.Fmath
println(short[]) - Static method in class umcg.genetica.math.Fmath
println(byte[]) - Static method in class umcg.genetica.math.Fmath
PROBE - Static variable in class umcg.genetica.io.trityper.QTLTextFile
ProbeAnnotation - Class in umcg.genetica.io.trityper
ProbeAnnotation() - Constructor for class umcg.genetica.io.trityper.ProbeAnnotation
ProbeAnnotation(String) - Constructor for class umcg.genetica.io.trityper.ProbeAnnotation
ProbeAnnotation - Class in umcg.genetica.io.trityper.probeannotation
ProbeAnnotation() - Constructor for class umcg.genetica.io.trityper.probeannotation.ProbeAnnotation
probeannotation - Variable in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDatasetSettings
PROBECHR - Static variable in class umcg.genetica.io.trityper.QTLTextFile
PROBELOC - Static variable in class umcg.genetica.io.trityper.QTLTextFile
ProbeTranslation - Class in umcg.genetica.io.trityper.probeannotation
ProbeTranslation() - Constructor for class umcg.genetica.io.trityper.probeannotation.ProbeTranslation
ProgressBar - Class in umcg.genetica.console
ProgressBar(long) - Constructor for class umcg.genetica.console.ProgressBar
ProgressBar(long, String) - Constructor for class umcg.genetica.console.ProgressBar
pruneAndReorderSamples(List<String>) - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
pruneGenotypeToExpressionCouplings() - Method in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDataset
pToZ(double) - Static method in class umcg.genetica.math.stats.ZScores: Returns the absolute Z-score for a given p-value using a normal distribution.
put(String, int, E) - Method in class umcg.genetica.collections.ChrPosMap
put(String, Integer, E) - Method in class umcg.genetica.collections.ChrPosTreeMap
putAnnotationInformation(String, String) - Method in class umcg.genetica.methylation.SoftfileAnnotation
PVAL - Static variable in class umcg.genetica.io.trityper.QTLTextFile

Q

Q_ELECTRON - Static variable in class umcg.genetica.math.Fmath
QTLTextFile - Class in umcg.genetica.io.trityper
QTLTextFile(String, boolean) - Constructor for class umcg.genetica.io.trityper.QTLTextFile
QTLTextFile(String, boolean, boolean) - Constructor for class umcg.genetica.io.trityper.QTLTextFile
QuantileNormAdressingNaValuesAfterInitialQN(DoubleMatrixDataset<String, String>, boolean, boolean, boolean) - Static method in class umcg.genetica.math.stats.QuantileNormalization: Quantile normalize data where missing values are allowed Do QN on all non-missing values, after which the missing values are replaced and a second QN is performed.
QuantileNormAdressingNaValuesBeforeQN(double[][], boolean, boolean) - Static method in class umcg.genetica.math.stats.QuantileNormalization: Quantile normalize data where missing values are allowed.
QuantileNormalization - Class in umcg.genetica.math.stats
QuantileNormalization() - Constructor for class umcg.genetica.math.stats.QuantileNormalization
quantilenormalize - Variable in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDatasetSettings
quantilenormalize(double[][]) - Static method in class umcg.genetica.math.stats.QuantileNormalization: Quantile normalize a double[][] double[probes][sample]
quartToLitre(double) - Static method in class umcg.genetica.math.Fmath
quartUKtoUS(double) - Static method in class umcg.genetica.math.Fmath
quartUStoUK(double) - Static method in class umcg.genetica.math.Fmath
quicksort(T[]) - Static method in class umcg.genetica.util.MultiThreadedInPlaceQuickSort: Main method used for sorting from clients.
qvalue(double[], Double) - Static method in class umcg.genetica.math.stats.QValues
qvalue(double[], double[], Double, boolean, Integer, QValues.SMOOTHER, boolean) - Static method in class umcg.genetica.math.stats.QValues
QValues - Class in umcg.genetica.math.stats
QValues() - Constructor for class umcg.genetica.math.stats.QValues
QValues.SMOOTHER - Enum in umcg.genetica.math.stats

R

R - Static variable in class umcg.genetica.io.bin.BinaryFile
R - Static variable in class umcg.genetica.io.text.TextFile
R - Static variable in class umcg.genetica.io.trityper.bin.BinaryGZipFloatMatrix
R - Static variable in class umcg.genetica.io.trityper.bin.BinaryResultProbeSummary
R - Static variable in class umcg.genetica.io.trityper.bin.BinaryResultSNPSummary
R_GAS - Static variable in class umcg.genetica.math.Fmath
radialFrequencyToFrequency(double) - Static method in class umcg.genetica.math.Fmath
radToDeg(double) - Static method in class umcg.genetica.math.Fmath
raiseElementsToPower(double[], double) - Static method in class umcg.genetica.math.Fmath
raiseElementsToPower(double[], int) - Static method in class umcg.genetica.math.Fmath
raiseElementsToPower(float[], float) - Static method in class umcg.genetica.math.Fmath
raiseElementsToPower(float[], int) - Static method in class umcg.genetica.math.Fmath
RandomAccessFile - Class in umcg.genetica.io.bin: A buffered drop-in replacement for java.io.RandomAccessFile.
RandomAccessFile(String, int) - Constructor for class umcg.genetica.io.bin.RandomAccessFile: Create a new buffered random-access file with a default buffer size.
RandomAccessFile(String, String) - Constructor for class umcg.genetica.io.bin.RandomAccessFile: Creates a random access file stream to read from, and optionally to write to, a file with the specified name.
RandomAccessFile(File, String) - Constructor for class umcg.genetica.io.bin.RandomAccessFile: Creates a random access file stream to read from, and optionally to write to, the file specified by the File argument.
RandomAccessFile(File, String, int) - Constructor for class umcg.genetica.io.bin.RandomAccessFile: Create a new buffered random-access file with a specified buffer size.
RandomAccessFile(String, int, int) - Constructor for class umcg.genetica.io.bin.RandomAccessFile: Create a new buffered random-access file with a specified buffer size.
Range - Interface in umcg.genetica.collections.intervaltree
RangeEndReverseComparator - Class in umcg.genetica.collections.intervaltree
RangeEndReverseComparator() - Constructor for class umcg.genetica.collections.intervaltree.RangeEndReverseComparator
RangeStartComparator - Class in umcg.genetica.collections.intervaltree
RangeStartComparator() - Constructor for class umcg.genetica.collections.intervaltree.RangeStartComparator
rank(double[], boolean) - Method in class umcg.genetica.util.RankArray
rank(float[], boolean) - Method in class umcg.genetica.util.RankArray
rank(double[]) - Method in class umcg.genetica.util.RankDoubleArray
rank(int[]) - Method in class umcg.genetica.util.RankIntArray
rankAllExpressionData(boolean) - Method in class umcg.genetica.io.trityper.TriTyperExpressionData: Ranks all the expressiondata available in rawData
RankArray - Class in umcg.genetica.util
RankArray() - Constructor for class umcg.genetica.util.RankArray
rankCorrelate(double[], double[]) - Static method in class umcg.genetica.math.stats.Correlation
RankDoubleArray - Class in umcg.genetica.util
RankDoubleArray() - Constructor for class umcg.genetica.util.RankDoubleArray
RankIntArray - Class in umcg.genetica.util
RankIntArray() - Constructor for class umcg.genetica.util.RankIntArray
rawData - Variable in class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
read() - Method in class com.mastfrog.util.streams.HashingInputStream
read(byte[], int, int) - Method in class com.mastfrog.util.streams.HashingInputStream
read(byte[]) - Method in class com.mastfrog.util.streams.HashingInputStream
read() - Method in class umcg.genetica.io.bin.BinaryFile
READ - Static variable in class umcg.genetica.io.bin.RandomAccessFile: Read from the file.
read() - Method in class umcg.genetica.io.bin.RandomAccessFile: Read a byte of data from the file, blocking until data is available.
read(byte[], int, int) - Method in class umcg.genetica.io.bin.RandomAccessFile: Read up to len bytes into an array, at a specified offset.
read(byte[]) - Method in class umcg.genetica.io.bin.RandomAccessFile: Read up to b.length( ) bytes into an array.
read(String) - Method in class umcg.genetica.io.gwascatalog.GWASCatalog
read(long, long, int) - Method in class umcg.genetica.io.trityper.bin.BinaryGZipFloatMatrix
read() - Method in class umcg.genetica.io.trityper.QTLTextFile
readAllProbes() - Method in class umcg.genetica.io.trityper.bin.BinaryResultProbeSummary
readAllSNPs() - Method in class umcg.genetica.io.trityper.bin.BinaryResultSNPSummary
readAnnotationFile(String, int, int) - Static method in class umcg.genetica.io.probemapping.reading: Read annotation file.
readAnnotationFileArrayList(String, int, int, int, boolean, int) - Static method in class umcg.genetica.io.probemapping.reading: Read annotation file Supply int key and int for value
readAnnotationFileHash(String, boolean, int, int, int) - Static method in class umcg.genetica.io.probemapping.reading: Read annotation file Supply int key and int for value
readAnnotationFileHashMap(String, boolean, int, int, int, int, int) - Static method in class umcg.genetica.io.probemapping.reading: Read annotation file Supply int key and int for value
readAnnotationFileHashMap2(String, boolean, int, int, int, int, int) - Static method in class umcg.genetica.io.probemapping.reading
readAsArray() - Method in class umcg.genetica.io.text.TextFile
readAsArray(int, Pattern) - Method in class umcg.genetica.io.text.TextFile
readAsArrayList() - Method in class umcg.genetica.io.text.TextFile
readAsArrayList(int, Pattern) - Method in class umcg.genetica.io.text.TextFile
readAsHashMap(int, int) - Method in class umcg.genetica.io.text.TextFile
readAsHashMap(int, int[], String) - Method in class umcg.genetica.io.text.TextFile
readAsHashMap(int, int, Pattern) - Method in class umcg.genetica.io.text.TextFile
readAsPairs(int, int) - Method in class umcg.genetica.io.text.TextFile
readAsSet(int, Pattern) - Method in class umcg.genetica.io.text.TextFile
readAsTriple(int, int, int) - Method in class umcg.genetica.io.text.TextFile
readBool() - Method in class umcg.genetica.io.bin.BinaryFile
readBoolean() - Method in class umcg.genetica.io.bin.RandomAccessFile: Reads a boolean from this file.
readByte() - Method in class umcg.genetica.io.bin.RandomAccessFile: Reads a signed 8-bit value from this file.
readChar() - Method in class umcg.genetica.io.bin.RandomAccessFile: Reads a Unicode character from this file.
readDeflated(long, long, int) - Method in class umcg.genetica.io.trityper.bin.BinaryGZipFloatMatrix
readDouble() - Method in class umcg.genetica.io.bin.BinaryFile
readDouble() - Method in class umcg.genetica.io.bin.RandomAccessFile: Reads a double from this file.
readDoubleMatrixFile(String, Set<String>) - Static method in class umcg.genetica.io.probemapping.reading: Read double matrix file restricting to given rows Eigenvector file / pc file / probe matrix
readExpectedSize(int) - Method in class umcg.genetica.io.trityper.QTLTextFile
readFilterHash(String) - Static method in class umcg.genetica.io.probemapping.reading: Read one file into HashSet
readFilterHash2(String[]) - Static method in class umcg.genetica.io.probemapping.reading: Read multiple file into HashSet
readFloat() - Method in class umcg.genetica.io.bin.BinaryFile
readFloat() - Method in class umcg.genetica.io.bin.RandomAccessFile: Reads a float from this file.
readFully(byte[]) - Method in class umcg.genetica.io.bin.RandomAccessFile: Reads b.length bytes from this file into the byte array.
readFully(byte[], int, int) - Method in class umcg.genetica.io.bin.RandomAccessFile: Reads exactly len bytes from this file into the byte array.
readGeneNamesForProbes(String, List<String>) - Static method in class umcg.genetica.methylation.AssociatingPcasWithAnnotation
readGTFAnnotationFileHash(String, int) - Static method in class umcg.genetica.io.probemapping.reading: read GTF file (gene code information)
reading - Class in umcg.genetica.io.probemapping
reading() - Constructor for class umcg.genetica.io.probemapping.reading
readInMultipleSamFiles(String, String) - Static method in class umcg.genetica.io.probemapping.reading: Read sam files
readInMultipleSamFiles2(String, String, int) - Static method in class umcg.genetica.io.probemapping.reading: Read sam files if there are more than maxDiff differences in the read the row is skipped
readInMultipleSamFiles2DG(String, String, int) - Static method in class umcg.genetica.io.probemapping.reading: Read sam files if there are more than maxDiff differences in the read the row is skipped Degenerate bases are not counted as a mismatch (removed from edit distance)
readInt() - Method in class umcg.genetica.io.bin.BinaryFile
readInt() - Method in class umcg.genetica.io.bin.RandomAccessFile: Reads a signed 32-bit integer from this file.
readInteractionResults(String, String, String) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
readInteractionResults(long) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
readLine() - Method in class umcg.genetica.io.bin.RandomAccessFile: Reads the next line of text from this file.
readLine() - Method in class umcg.genetica.io.text.TextFile
readLineElems(Pattern) - Method in class umcg.genetica.io.text.TextFile: This method is a wrapper for readLineElemsReturnReference: this method returns default substrings delimited by Pattern p.
readLineElemsIterable(Pattern) - Method in class umcg.genetica.io.text.TextFile
readLineElemsReturnObjects(Pattern) - Method in class umcg.genetica.io.text.TextFile: This method returns a new object for each of the splitted elements, instead of the default action, in which each substring is backed by the original full-length String.
readLineElemsReturnReference(Pattern) - Method in class umcg.genetica.io.text.TextFile: This method returns default substrings delimited by Pattern p.
readList() - Method in class umcg.genetica.io.trityper.QTLTextFile
readListToArrayList(String) - Static method in class umcg.genetica.io.probemapping.reading: Read one file into HashSet
readLong() - Method in class umcg.genetica.io.bin.BinaryFile
readLong() - Method in class umcg.genetica.io.bin.RandomAccessFile: Reads a signed 64-bit integer from this file.
readMetaAnalysisResults(String, boolean, int, int, int, int) - Static method in class umcg.genetica.io.probemapping.reading
readMultipleSNPAnnotationFiles(String, double, boolean) - Static method in class umcg.genetica.io.probemapping.reading: Read SNP information files
readMultipleSNPAnnotationFiles2(String, double, boolean) - Static method in class umcg.genetica.io.probemapping.reading: Read SNP information files
readMultipleSNPAnnotationFiles3(String, double, boolean) - Static method in class umcg.genetica.io.probemapping.reading: Read SNP information files
readMultipleSNPAnnotationFilesSmall(String, double, boolean) - Static method in class umcg.genetica.io.probemapping.reading: Read SNP information files
readNextProbe() - Method in class umcg.genetica.io.trityper.bin.BinaryResultProbeSummary
readNextSNP() - Method in class umcg.genetica.io.trityper.bin.BinaryResultSNPSummary
readQtlResults(String, String) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
readShort() - Method in class umcg.genetica.io.bin.RandomAccessFile: Reads a signed 16-bit number from this file.
readSNPZScores(BinaryResultSNP) - Method in class umcg.genetica.io.trityper.bin.BinaryResultDataset
readString() - Method in class umcg.genetica.io.bin.BinaryFile
readUnsignedByte() - Method in class umcg.genetica.io.bin.RandomAccessFile: Reads an unsigned 8-bit number from this file.
readUnsignedShort() - Method in class umcg.genetica.io.bin.RandomAccessFile: Reads an unsigned 16-bit number from this file.
readUTF() - Method in class umcg.genetica.io.bin.RandomAccessFile: Reads in a string from this file.
readVariantGeneCovariateResults(String, String, String) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
readVariantGeneResults(String, String) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
recalculateHashMaps() - Method in class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
recalculateHashMaps() - Method in class umcg.genetica.math.matrix.DoubleMatrixDatasetAC: Deprecated.
recalculateHashMaps() - Method in class umcg.genetica.math.matrix.DoubleMatrixDatasetRA: Deprecated.
ReferenceGenomeFasta - Class in umcg.genetica.io.fasta
ReferenceGenomeFasta(File, Set<String>) - Constructor for class umcg.genetica.io.fasta.ReferenceGenomeFasta
Regression - Class in umcg.genetica.math.stats
Regression() - Constructor for class umcg.genetica.math.stats.Regression
RegulomeDbEntry - Class in umcg.genetica.io.regulomedb
RegulomeDbEntry(String) - Constructor for class umcg.genetica.io.regulomedb.RegulomeDbEntry
RegulomeDbFile - Class in umcg.genetica.io.regulomedb
RegulomeDbFile(File) - Constructor for class umcg.genetica.io.regulomedb.RegulomeDbFile
RegulomeDbFiles - Class in umcg.genetica.io.regulomedb
RegulomeDbFiles(ArrayList<RegulomeDbFile>) - Constructor for class umcg.genetica.io.regulomedb.RegulomeDbFiles
RegulomeDbFiles(Collection<File>) - Constructor for class umcg.genetica.io.regulomedb.RegulomeDbFiles
RegulomeDbIterator - Class in umcg.genetica.io.regulomedb
RegulomeDbIterator(RegulomeDbFile) - Constructor for class umcg.genetica.io.regulomedb.RegulomeDbIterator
RegulomeDbIterator(Collection<RegulomeDbFile>) - Constructor for class umcg.genetica.io.regulomedb.RegulomeDbIterator
RegulomeDbSupportingData - Class in umcg.genetica.io.regulomedb
RegulomeDbSupportingData(String) - Constructor for class umcg.genetica.io.regulomedb.RegulomeDbSupportingData
remove(String, int) - Method in class umcg.genetica.collections.ChrPosMap
remove(String, Integer) - Method in class umcg.genetica.collections.ChrPosTreeMap
remove() - Method in class umcg.genetica.genomicboundaries.GenomicBoundariesIterator
remove() - Method in class umcg.genetica.io.binInteraction.BinaryInteractionCovariateIterator
remove() - Method in class umcg.genetica.io.gtf.GffElementIterator
remove() - Method in class umcg.genetica.io.regulomedb.RegulomeDbIterator
RemoveColumns(DoubleMatrixDataset<String, String>, HashSet<String>) - Static method in class umcg.genetica.math.matrix.MatrixHandling: Remove samples on forehand
RemoveColumns(DoubleMatrixDataset<String, String>, HashSet<String>) - Static method in class umcg.genetica.math.matrix2.MatrixHandling: Remove samples on forehand
removeColumnsWithNaNs() - Method in class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
RemoveColumnsWithToManyMissingValues(DoubleMatrixDataset<String, String>, int) - Static method in class umcg.genetica.math.matrix.MatrixHandling: Remove columns with to many missing values
RemoveColumnsWithToManyMissingValues(DoubleMatrixDataset<String, String>, int, double) - Static method in class umcg.genetica.math.matrix2.MatrixHandling: Remove columns with to many missing values
RemoveDuplicateRowNames(DoubleMatrixDataset<String, String>) - Static method in class umcg.genetica.math.matrix.MatrixHandling
RemoveDuplicatesSamples(DoubleMatrixDataset<String, String>, boolean) - Static method in class umcg.genetica.math.matrix.MatrixHandling: Remove identical samples, based on name and/or based on all expression value (advanced = true)
RemoveDuplicatesSamples(DoubleMatrixDataset<String, String>) - Static method in class umcg.genetica.math.matrix2.MatrixHandling: Remove identical samples, based on all expression values
RemoveProbes(DoubleMatrixDataset<String, String>, HashSet<String>) - Static method in class umcg.genetica.math.matrix.MatrixHandling: Remove probes without correct mapping known on forehand
RemoveProbes(DoubleMatrixDataset<String, String>, HashSet<String>) - Static method in class umcg.genetica.math.matrix2.MatrixHandling: Remove probes without correct mapping known on forehand
RemoveRows(DoubleMatrixDataset<String, String>, HashSet<String>) - Static method in class umcg.genetica.math.matrix.MatrixHandling: Remove rows without correct mapping known on forehand
RemoveRows(DoubleMatrixDataset<String, String>, HashSet<String>) - Method in class umcg.genetica.math.matrix2.MatrixHandling: Remove rows without correct mapping known on forehand
RemoveRowsWithToManyMissingValues(DoubleMatrixDataset<String, String>, int) - Static method in class umcg.genetica.math.matrix.MatrixHandling: Remove rows with to many missing values
RemoveRowsWithToManyMissingValues(DoubleMatrixDataset<String, String>, int, double) - Static method in class umcg.genetica.math.matrix2.MatrixHandling: Remove rows with to many missing values
RemoveSamples(DoubleMatrixDataset<String, String>, HashSet<String>) - Static method in class umcg.genetica.math.matrix.MatrixHandling: Remove samples on forehand
RemoveSamples(DoubleMatrixDataset<String, String>, HashSet<String>) - Static method in class umcg.genetica.math.matrix2.MatrixHandling: Remove samples on forehand
removeSubBoundaries() - Method in class umcg.genetica.genomicboundaries.GenomicBoundaries: Method to remove boundaries that are sub boundaries of other boundaries.
RenameCols(DoubleMatrixDataset<String, String>, HashMap<String, String>) - Static method in class umcg.genetica.math.matrix.MatrixHandling
RenameCols(DoubleMatrixDataset<?, String>, HashMap<String, String>) - Static method in class umcg.genetica.math.matrix2.MatrixHandling
RenameRows(DoubleMatrixDataset<String, ?>, HashMap<String, String>) - Static method in class umcg.genetica.math.matrix2.MatrixHandling
reorderCols(LinkedHashMap<C, Integer>) - Method in class umcg.genetica.math.matrix2.DoubleMatrixDataset
ReorderRows(DoubleMatrixDataset<String, String>, HashMap<String, Integer>) - Static method in class umcg.genetica.math.matrix.MatrixHandling: Order rows to a index
reorderRows(LinkedHashMap<R, Integer>) - Method in class umcg.genetica.math.matrix2.DoubleMatrixDataset
ReplaceMissingValues(double[][], boolean) - Static method in class umcg.genetica.math.matrix.MatrixHandling: Replace missing values in the double matrix per sample.
ReplaceMissingValuesPerColumn(DoubleMatrix2D, boolean, double) - Static method in class umcg.genetica.math.matrix2.MatrixHandling: Replace missing values in the double matrix per sample.
ReplaceMissingValuesPerRow(DoubleMatrix2D, boolean, double) - Static method in class umcg.genetica.math.matrix2.MatrixHandling: Replace missing values in the double matrix per sample.
ReplaceNullToZero(double[][]) - Static method in class umcg.genetica.math.matrix.MatrixHandling: Replace null's with zero's.
ReplaceZerosToNull(double[][]) - Static method in class umcg.genetica.math.matrix.MatrixHandling: Replace zero's with nulls.
ReplaceZerosToNull(DoubleMatrix2D) - Static method in class umcg.genetica.math.matrix2.MatrixHandling: Replace zero's with nulls.
rescaleBetavalue(DoubleMatrix2D) - Static method in class umcg.genetica.methylation.ConvertBetaAndMvalues
rescaleValue(DoubleMatrix2D, Double) - Static method in class umcg.genetica.io.trityper.ConvertDoubleMatrixDataToTriTyper
reset() - Method in class com.mastfrog.util.streams.HashingInputStream
resetData(double[], double[]) - Method in class umcg.genetica.math.interpolation.CubicSpline
resetGenotypeToExpressionCouplings() - Method in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDataset
RETURN_D_PRIME - Static variable in class umcg.genetica.io.trityper.util.DetermineLD
RETURN_R_SQUARED - Static variable in class umcg.genetica.io.trityper.util.DetermineLD
returnWilcoxonMannWhitneyPValue(double[], double[]) - Method in class umcg.genetica.math.stats.WilcoxonMannWhitney
reverse(String) - Static method in class umcg.genetica.text.Strings
reverseArray(double[]) - Static method in class umcg.genetica.math.Fmath
reverseArray(float[]) - Static method in class umcg.genetica.math.Fmath
reverseArray(int[]) - Static method in class umcg.genetica.math.Fmath
reverseArray(long[]) - Static method in class umcg.genetica.math.Fmath
reverseArray(char[]) - Static method in class umcg.genetica.math.Fmath
RND - Static variable in class umcg.genetica.util.InplaceArrayQuickSort
rowObjects - Variable in class umcg.genetica.math.matrix.DoubleMatrixDatasetAC: Deprecated.
rows() - Method in class umcg.genetica.math.matrix2.DoubleMatrixDataset
rowsToInclude - Variable in class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
rowsToInclude - Variable in class umcg.genetica.math.matrix.DoubleMatrixDatasetRA: Deprecated.
rsToChrPos - Variable in class umcg.genetica.ncbi.dbsnp.SNPAnnotation
RunTimer - Class in umcg.genetica.util
RunTimer(RunTimer.Granularity) - Constructor for class umcg.genetica.util.RunTimer
RunTimer() - Constructor for class umcg.genetica.util.RunTimer
RunTimer.Granularity - Enum in umcg.genetica.util

S

s - Variable in class umcg.genetica.containers.SortableSNP
sameQTL(EQTL) - Method in class umcg.genetica.io.trityper.EQTL
save(String) - Method in class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
save(File) - Method in class umcg.genetica.math.matrix.SymmetricByteDistanceMatrix
save(File) - Method in class umcg.genetica.math.matrix.SymmetricShortDistanceMatrix
save(File) - Method in class umcg.genetica.math.matrix2.DoubleMatrixDataset
save(String) - Method in class umcg.genetica.math.matrix2.DoubleMatrixDataset
saveDice(String) - Method in class umcg.genetica.math.matrix2.DoubleMatrixDataset
scaleColum(DoubleMatrix2D) - Static method in class umcg.genetica.math.matrix2.MatrixTools
ScatterPlot - Class in umcg.genetica.graphics
ScatterPlot(int, int, double[], double[], ScatterPlot.OUTPUTFORMAT, String) - Constructor for class umcg.genetica.graphics.ScatterPlot
ScatterPlot(int, int, double, double, double[], double[], ScatterPlot.OUTPUTFORMAT, String) - Constructor for class umcg.genetica.graphics.ScatterPlot
ScatterPlot(int, int, double[], double[], int[], String[], Color[], ScatterPlot.OUTPUTFORMAT, String, String, String, boolean) - Constructor for class umcg.genetica.graphics.ScatterPlot
ScatterPlot.OUTPUTFORMAT - Enum in umcg.genetica.graphics
searchPosition(String, int) - Method in class umcg.genetica.collections.intervaltree.PerChrIntervalTree
sec(double) - Static method in class umcg.genetica.math.Fmath
sech(double) - Static method in class umcg.genetica.math.Fmath
seek(long) - Method in class umcg.genetica.io.bin.RandomAccessFile: Set the position in the file for the next read or write.
selectGenotypes(int[]) - Method in class umcg.genetica.io.trityper.SNP
selectGenotypes(short[], boolean, boolean) - Method in class umcg.genetica.io.trityper.SNP
selectGenotypes(int[], boolean, boolean) - Method in class umcg.genetica.io.trityper.SNP
selectionSort(double[]) - Static method in class umcg.genetica.math.Fmath
selectionSort(float[]) - Static method in class umcg.genetica.math.Fmath
selectionSort(int[]) - Static method in class umcg.genetica.math.Fmath
selectionSort(long[]) - Static method in class umcg.genetica.math.Fmath
selectionSort(double[], double[], int[]) - Static method in class umcg.genetica.math.Fmath
selectionSort(double[], double[], double[], double[]) - Static method in class umcg.genetica.math.Fmath
selectionSort(float[], float[], float[], float[]) - Static method in class umcg.genetica.math.Fmath
selectionSort(long[], long[], long[], long[]) - Static method in class umcg.genetica.math.Fmath
selectionSort(int[], int[], int[], int[]) - Static method in class umcg.genetica.math.Fmath
selectionSort(double[], long[], double[], long[]) - Static method in class umcg.genetica.math.Fmath
selectionSort(long[], double[], long[], double[]) - Static method in class umcg.genetica.math.Fmath
selectionSort(double[], int[], double[], int[]) - Static method in class umcg.genetica.math.Fmath
selectionSort(int[], double[], int[], double[]) - Static method in class umcg.genetica.math.Fmath
selectionSort(long[], int[], long[], int[]) - Static method in class umcg.genetica.math.Fmath
selectionSort(int[], long[], int[], long[]) - Static method in class umcg.genetica.math.Fmath
selectSNPsWithSimilarMAFsAsRealInputSNPs(String[]) - Method in class umcg.genetica.gwas.Independifier
selectSort(double[], double[], int[]) - Static method in class umcg.genetica.math.Fmath
selectSortArrayList(double[]) - Static method in class umcg.genetica.math.Fmath
selectSortVector(double[]) - Static method in class umcg.genetica.math.Fmath
semicolon - Static variable in class umcg.genetica.io.text.TextFile
semicolon - Static variable in class umcg.genetica.text.Strings
SEPARATOR - Static variable in class umcg.genetica.console.ConsoleGUIElems
set(long) - Method in class umcg.genetica.console.ProgressBar
set(int, int, int) - Method in class umcg.genetica.math.matrix.SymmetricByteDistanceMatrix
set(int, int, int) - Method in class umcg.genetica.math.matrix.SymmetricShortDistanceMatrix
setAccession(String) - Method in class umcg.genetica.methylation.SoftfileAnnotation
setAllCovariants(boolean) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFileConstructorBuilder
setAllele1(int, int, byte) - Method in class umcg.genetica.io.trityper.WGAFileMatrixGenotype
setAllele1(int, int, byte[]) - Method in class umcg.genetica.io.trityper.WGAFileMatrixGenotype
setAllele2(int, int, byte) - Method in class umcg.genetica.io.trityper.WGAFileMatrixGenotype
setAllele2(int, int, byte[]) - Method in class umcg.genetica.io.trityper.WGAFileMatrixGenotype
setAlleleAssessed(String) - Method in class umcg.genetica.io.trityper.EQTL
setAlleleCodes(byte[]) - Method in class umcg.genetica.io.trityper.SNP
setAllElements(int) - Method in class umcg.genetica.math.matrix.SymmetricByteDistanceMatrix
setAllElements(int) - Method in class umcg.genetica.math.matrix.SymmetricShortDistanceMatrix
setAlleles(byte[]) - Method in class umcg.genetica.io.trityper.bin.BinaryResultSNP
setAlleles(String) - Method in class umcg.genetica.io.trityper.EQTL
setAlleles(byte[], byte[], Boolean[], Boolean[]) - Method in class umcg.genetica.io.trityper.SNP
setAlleles(byte[], byte[]) - Method in class umcg.genetica.io.trityper.SNP
setAlleles(int, byte[], byte[]) - Method in class umcg.genetica.io.trityper.WGAFileMatrixGenotype
setAnnotation(String) - Method in class umcg.genetica.containers.Gene
setAnnotation(String) - Method in class umcg.genetica.io.trityper.bin.BinaryResultProbe
setAnnotation(String[]) - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
setAnnotationInformation(LinkedHashMap<String, String>) - Method in class umcg.genetica.methylation.SoftfileAnnotation
setAssessedAllele(Byte) - Method in class umcg.genetica.io.trityper.bin.BinaryResultSNP
setAssociatedTraits(HashSet<GWASTrait>) - Method in class umcg.genetica.io.gwascatalog.GWASSNP
setBeta(String) - Method in class umcg.genetica.io.trityper.EQTL
setChr(byte) - Method in class umcg.genetica.io.gwascatalog.GWASSNP
setChr(byte) - Method in class umcg.genetica.io.trityper.bin.BinaryResultProbe
setChr(Byte) - Method in class umcg.genetica.io.trityper.bin.BinaryResultSNP
setChr(short[]) - Method in class umcg.genetica.io.trityper.ProbeAnnotation
setChr(byte) - Method in class umcg.genetica.io.trityper.SNP
setChr(byte[]) - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
setChrEnd(int[]) - Method in class umcg.genetica.io.trityper.ProbeAnnotation
setChromosomeHash(HashMap<String, Chromosome>) - Method in class umcg.genetica.ensembl.Features
setChrpos(Integer) - Method in class umcg.genetica.io.trityper.bin.BinaryResultSNP
setChrPos(int) - Method in class umcg.genetica.io.trityper.SNP
setChrStart(int[]) - Method in class umcg.genetica.io.trityper.ProbeAnnotation
setChrStart(int[]) - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
setChrStop(int[]) - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
setCohorts(BinaryInteractionCohort[]) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFileConstructorBuilder
setColNames(String[]) - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
setColNameToId(TObjectIntHashMap<String>) - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
setColObjects(List<C>) - Method in class umcg.genetica.math.matrix2.DoubleMatrixDataset
setConfineToProbesThatMapToAnyChromosome(boolean) - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
setConfineToProbesThatMapToChromosome(Integer) - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
setCorrelations(Double[]) - Method in class umcg.genetica.io.trityper.EQTL
setCovariates(String[]) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFileConstructorBuilder
setCovariatesTested(int[][]) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFileConstructorBuilder
setCr(Double) - Method in class umcg.genetica.io.trityper.bin.BinaryResultSNP
setCR(Double) - Method in class umcg.genetica.io.trityper.SNP
setDatasets(String[]) - Method in class umcg.genetica.io.trityper.EQTL
setDatasetsSamples(Integer[]) - Method in class umcg.genetica.io.trityper.EQTL
setDatasetZScores(Double[]) - Method in class umcg.genetica.io.trityper.EQTL
setDeriv(double, double) - Method in class umcg.genetica.math.interpolation.CubicSpline
setDeriv(double[]) - Method in class umcg.genetica.math.interpolation.CubicSpline
setDerivLimits(double, double) - Method in class umcg.genetica.math.interpolation.CubicSpline
setDerivLimits() - Method in class umcg.genetica.math.interpolation.CubicSpline
setDescription(String) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFileCreator
setDosage(byte[]) - Method in class umcg.genetica.io.trityper.SNP
setDosage(int, int, byte[]) - Method in class umcg.genetica.io.trityper.WGAFileMatrixImputedDosage
setDosage(int, int, byte) - Method in class umcg.genetica.io.trityper.WGAFileMatrixImputedDosage
setDosageFileName(String) - Method in class umcg.genetica.io.trityper.TriTyperGenotypeData
setElement(R, C, double) - Method in class umcg.genetica.math.matrix2.DoubleMatrixDataset: Set a element of the dataset.
setEnd(int) - Method in class umcg.genetica.containers.Exon
setEnd(int) - Method in class umcg.genetica.containers.Gene
setEnd(int) - Method in class umcg.genetica.containers.Transcript
setExonHash(HashMap<String, Exon>) - Method in class umcg.genetica.ensembl.Features
setExonRank(Exon, Integer) - Method in class umcg.genetica.containers.Transcript
setExons(HashMap<String, Exon>) - Method in class umcg.genetica.containers.Transcript
setExpressionData(TriTyperExpressionData) - Method in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDataset
setExpressionDataLoadedCorrectly(boolean) - Method in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDataset
setFC(String) - Method in class umcg.genetica.io.trityper.EQTL
setFDR(double) - Method in class umcg.genetica.io.trityper.EQTL
setFileDescription(String) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFileConstructorBuilder
setFlippedZscoreStored(boolean) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFileConstructorBuilder
setGCScore(int, int, byte[]) - Method in class umcg.genetica.io.trityper.WGAFileMatrixRawData
setGeneHash(HashMap<String, Gene>) - Method in class umcg.genetica.ensembl.Features
setGeneNames(String[]) - Method in class umcg.genetica.graphics.ForestPlot
setGenes(HashMap<String, Gene>) - Method in class umcg.genetica.containers.Chromosome
setGenes(ArrayList<Gene>) - Method in class umcg.genetica.containers.Chromosome
setGenes(BinaryInteractionGene[]) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFileConstructorBuilder
setGenotypeData(TriTyperGenotypeData) - Method in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDataset
setGenotypeFileName(String) - Method in class umcg.genetica.io.trityper.TriTyperGenotypeData
setGenotypeFreq(int[]) - Method in class umcg.genetica.io.trityper.SNP
setGenotypeToExpressionCouplings(THashMap<String, String>) - Method in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDataset
setHashCols(LinkedHashMap<C, Integer>) - Method in class umcg.genetica.math.matrix2.DoubleMatrixDataset
setHashRows(LinkedHashMap<R, Integer>) - Method in class umcg.genetica.math.matrix2.DoubleMatrixDataset
setHwe(Double) - Method in class umcg.genetica.io.trityper.bin.BinaryResultSNP
setHWEP(Double) - Method in class umcg.genetica.io.trityper.SNP
setId(int) - Method in class umcg.genetica.io.gwascatalog.GWASSNP
setId(int) - Method in class umcg.genetica.io.trityper.bin.BinaryResultProbe
setId(Integer) - Method in class umcg.genetica.io.trityper.bin.BinaryResultSNP
setId(int) - Method in class umcg.genetica.io.trityper.SNP
setIncludeIndividuals(THashSet<String>) - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
setIndividualToId(TObjectIntHashMap<String>) - Method in class umcg.genetica.io.trityper.TriTyperGenotypeData
setInteractionFile(File) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFileConstructorBuilder
setInteractionResults(String, String, String, BinaryInteractionZscores) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
setInteractions(long) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFileConstructorBuilder
setIsCase(Boolean[]) - Method in class umcg.genetica.io.trityper.TriTyperGenotypeData
setIsFemale(Boolean[]) - Method in class umcg.genetica.io.trityper.TriTyperGenotypeData
setIsIncluded(Boolean[]) - Method in class umcg.genetica.io.trityper.TriTyperGenotypeData
setLoci(HashSet<GWASLocus>) - Method in class umcg.genetica.io.gwascatalog.GWASCatalog
setLocus(String) - Method in class umcg.genetica.io.gwascatalog.GWASSNP
setLocusToObj(HashMap<String, GWASLocus>) - Method in class umcg.genetica.io.gwascatalog.GWASCatalog
setM_location(String) - Method in class umcg.genetica.io.trityper.bin.BinaryResultDataset
setM_name(String) - Method in class umcg.genetica.io.trityper.bin.BinaryResultDataset
setMaf(Double) - Method in class umcg.genetica.io.trityper.bin.BinaryResultSNP
setMAF(Double) - Method in class umcg.genetica.io.trityper.SNP
setMappedGenes(HashSet<String>) - Method in class umcg.genetica.io.gwascatalog.GWASTrait
setMatrix(double[][]) - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
setMatrix(DoubleMatrix2D) - Method in class umcg.genetica.math.matrix2.DoubleMatrixDataset
setMatrix(double[][]) - Method in class umcg.genetica.math.matrix2.DoubleMatrixDataset
setMax(double) - Method in class umcg.genetica.io.ucsc.UCSCTrack
setMaxfloat(float) - Method in class umcg.genetica.io.trityper.bin.BinaryResultDataset
setMean(double) - Method in class umcg.genetica.io.ucsc.UCSCTrack
setMeshTerms(String) - Method in class umcg.genetica.methylation.SoftfileAnnotation
setMetaAnalysis(boolean) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFileConstructorBuilder
setMetaBeta(String) - Method in class umcg.genetica.io.trityper.EQTL
setMidpoint(int) - Method in class umcg.genetica.io.trityper.bin.BinaryResultProbe
setMin(double) - Method in class umcg.genetica.io.ucsc.UCSCTrack
setMinfloat(float) - Method in class umcg.genetica.io.trityper.bin.BinaryResultDataset
setMinorAllele(Byte) - Method in class umcg.genetica.io.trityper.bin.BinaryResultSNP
setMinorAllele(byte) - Method in class umcg.genetica.io.trityper.SNP
setName(String) - Method in class umcg.genetica.containers.Chromosome
setName(String) - Method in class umcg.genetica.containers.Exon
setName(String) - Method in class umcg.genetica.containers.Gene
setName(String) - Method in class umcg.genetica.containers.Transcript
setName(String) - Method in class umcg.genetica.io.gwascatalog.GWASSNP
setName(String) - Method in class umcg.genetica.io.trityper.bin.BinaryResultProbe
setName(String) - Method in class umcg.genetica.io.trityper.bin.BinaryResultSNP
setName(String) - Method in class umcg.genetica.io.trityper.SNP
setNormalQtlStored(boolean) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFileConstructorBuilder
setNrCalled(int) - Method in class umcg.genetica.io.trityper.SNP
setNumIndividuals(int) - Method in class umcg.genetica.io.trityper.BufferedSNPLoader
setNumIndividuals(int) - Method in class umcg.genetica.io.trityper.SNPLoader
setNumsamples(Integer) - Method in class umcg.genetica.io.trityper.bin.BinaryResultSNP
setParentChromosome(Chromosome) - Method in class umcg.genetica.containers.Exon
setParentChromosome(Chromosome) - Method in class umcg.genetica.containers.Gene
setParentChromosome(Chromosome) - Method in class umcg.genetica.containers.Transcript
setParentGene(Gene) - Method in class umcg.genetica.containers.Transcript
setParentTranscript(Transcript) - Method in class umcg.genetica.containers.Exon
setPassesQC(boolean) - Method in class umcg.genetica.io.trityper.SNP
setPathwayDefinitions(Pair<List<String>, List<List<String>>>) - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
setPosition(int) - Method in class umcg.genetica.io.gwascatalog.GWASSNP
setProbe(String) - Method in class umcg.genetica.io.trityper.EQTL
setProbeAnnotation(String[]) - Method in class umcg.genetica.io.trityper.ProbeAnnotation
setProbeChr(byte) - Method in class umcg.genetica.io.trityper.EQTL
setProbeChrPos(int) - Method in class umcg.genetica.io.trityper.EQTL
setProbeHUGO(String) - Method in class umcg.genetica.io.trityper.EQTL
setProbeMeans(Double[]) - Method in class umcg.genetica.io.trityper.EQTL
setProbes(BinaryResultProbe[]) - Method in class umcg.genetica.io.trityper.bin.BinaryResultDataset
setProbes(String[]) - Method in class umcg.genetica.io.trityper.ProbeAnnotation
setProbeToProbeId(HashMap<String, Integer>) - Method in class umcg.genetica.io.trityper.ProbeAnnotation
setProbeVariance(Double[]) - Method in class umcg.genetica.io.trityper.EQTL
setProtein(String) - Method in class umcg.genetica.containers.Transcript
setPublicationToObj(HashMap<String, GWASPublication>) - Method in class umcg.genetica.io.gwascatalog.GWASCatalog
setPublishedIn(HashSet<GWASPublication>) - Method in class umcg.genetica.io.gwascatalog.GWASSNP
setPvalue(double) - Method in class umcg.genetica.io.trityper.EQTL
setPvalueAbs(double) - Method in class umcg.genetica.io.trityper.EQTL
setPValueAssociatedWithTrait(GWASSNP, GWASTrait, Double) - Method in class umcg.genetica.io.gwascatalog.GWASPublication
setPValueAssociatedWithTrait(GWASTrait, Double) - Method in class umcg.genetica.io.gwascatalog.GWASSNP
setQtlResults(String, String, BinaryInteractionQtlZscores) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFile
setQuick(long, byte) - Method in class umcg.genetica.io.fasta.LargeByteArray: Set value at index.
setR(int, int, byte[]) - Method in class umcg.genetica.io.trityper.WGAFileMatrixRawData
setRawData(double[][]) - Method in class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
setReadOnly(boolean) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFileConstructorBuilder
setReportedGenes(HashSet<String>) - Method in class umcg.genetica.io.gwascatalog.GWASTrait
setRiskAllele(HashMap<GWASTrait, String>) - Method in class umcg.genetica.io.gwascatalog.GWASSNP
setRowNames(String[]) - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
setRowNameToId(TObjectIntHashMap<String>) - Method in class umcg.genetica.io.trityper.TriTyperExpressionData
setRowObjects(List<R>) - Method in class umcg.genetica.math.matrix2.DoubleMatrixDataset
setRsChr(byte) - Method in class umcg.genetica.io.trityper.EQTL
setRsChrPos(int) - Method in class umcg.genetica.io.trityper.EQTL
setRsName(String) - Method in class umcg.genetica.io.trityper.EQTL
setSD(double) - Method in class umcg.genetica.io.ucsc.UCSCTrack
setSettings(TriTyperGeneticalGenomicsDatasetSettings) - Method in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDataset
setSnps(HashSet<GWASSNP>) - Method in class umcg.genetica.io.gwascatalog.GWASCatalog
setSnps(BinaryResultSNP[]) - Method in class umcg.genetica.io.trityper.bin.BinaryResultDataset
setSNPs(String[]) - Method in class umcg.genetica.io.trityper.TriTyperGenotypeData
setSnpToObj(HashMap<String, GWASSNP>) - Method in class umcg.genetica.io.gwascatalog.GWASCatalog
setSnpToSNPObject(TObjectIntHashMap<String>) - Method in class umcg.genetica.io.trityper.TriTyperGenotypeData
setStart(int) - Method in class umcg.genetica.containers.Exon
setStart(int) - Method in class umcg.genetica.containers.Gene
setStart(int) - Method in class umcg.genetica.containers.Transcript
setStart(int) - Method in class umcg.genetica.io.trityper.bin.BinaryResultProbe
setStartInteractionBlock(long) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFileConstructorBuilder
setStartQtlBlock(long) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFileConstructorBuilder
setStop(int) - Method in class umcg.genetica.io.trityper.bin.BinaryResultProbe
setStrand(int) - Method in class umcg.genetica.containers.Exon
setStrand(int) - Method in class umcg.genetica.containers.Gene
setStrand(int) - Method in class umcg.genetica.containers.Transcript
setStringToProbe(HashMap<String, BinaryResultProbe>) - Method in class umcg.genetica.io.trityper.bin.BinaryResultDataset
setStringToSNP(HashMap<String, BinaryResultSNP>) - Method in class umcg.genetica.io.trityper.bin.BinaryResultDataset
setTheta(int, int, byte[]) - Method in class umcg.genetica.io.trityper.WGAFileMatrixRawData
setTimeStamp(long) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFileConstructorBuilder
setTitle(String) - Method in class umcg.genetica.methylation.SoftfileAnnotation
setTraits(HashSet<GWASTrait>) - Method in class umcg.genetica.io.gwascatalog.GWASCatalog
setTraitToObj(HashMap<String, GWASTrait>) - Method in class umcg.genetica.io.gwascatalog.GWASCatalog
setTranscriptHash(HashMap<String, Transcript>) - Method in class umcg.genetica.ensembl.Features
setTranscripts(HashMap<String, Transcript>) - Method in class umcg.genetica.containers.Gene
setType(String) - Method in class umcg.genetica.io.trityper.EQTL
setUseAbsoluteZScore() - Method in class umcg.genetica.io.trityper.EQTL
setVariants(BinaryInteractionVariant[]) - Method in class umcg.genetica.io.binInteraction.BinaryInteractionFileConstructorBuilder
setZscore(double) - Method in class umcg.genetica.io.trityper.EQTL
setZscoreAbs(double) - Method in class umcg.genetica.io.trityper.EQTL
setzScoreIndex(Long) - Method in class umcg.genetica.io.trityper.bin.BinaryResultSNP
sha1(InputStream) - Static method in class com.mastfrog.util.streams.HashingInputStream
sha1(OutputStream) - Static method in class com.mastfrog.util.streams.HashingOutputStream
shortTOdouble(short[]) - Static method in class umcg.genetica.math.Fmath
shortTOfloat(short[]) - Static method in class umcg.genetica.math.Fmath
shortTOint(short[]) - Static method in class umcg.genetica.math.Fmath
shortTOlong(short[]) - Static method in class umcg.genetica.math.Fmath
sign(double) - Static method in class umcg.genetica.math.Fmath
sign(float) - Static method in class umcg.genetica.math.Fmath
sign(int) - Static method in class umcg.genetica.math.Fmath
sign(long) - Static method in class umcg.genetica.math.Fmath
sin(double, double, double, double, double, double) - Static method in class umcg.genetica.math.Fmath
sin(double, double, double) - Static method in class umcg.genetica.math.Fmath
sin(double) - Static method in class umcg.genetica.math.Fmath
sinc(double) - Static method in class umcg.genetica.math.Fmath
sinh(double) - Static method in class umcg.genetica.math.Fmath
size() - Method in class umcg.genetica.collections.ChrPosMap
size() - Method in class umcg.genetica.collections.ChrPosTreeMap
size() - Method in class umcg.genetica.collections.intervaltree.IntervalTree
size() - Method in class umcg.genetica.collections.intervaltree.PerChrIntervalTree
size() - Method in class umcg.genetica.io.ucsc.PeakFile
size() - Method in class umcg.genetica.io.ucsc.WigFile
size() - Method in class umcg.genetica.math.matrix.SymmetricByteDistanceMatrix
size() - Method in class umcg.genetica.math.matrix.SymmetricShortDistanceMatrix
sizeInteractionBlock - Variable in class umcg.genetica.io.binInteraction.BinaryInteractionFile
skipBytes(int) - Method in class umcg.genetica.io.bin.RandomAccessFile: Skips exactly n bytes of input.
SmoothSort - Class in umcg.genetica.util
SmoothSort() - Constructor for class umcg.genetica.util.SmoothSort
SNP - Static variable in class umcg.genetica.io.trityper.QTLTextFile
SNP - Class in umcg.genetica.io.trityper
SNP() - Constructor for class umcg.genetica.io.trityper.SNP
SNPAnnotation - Class in umcg.genetica.ncbi.dbsnp
SNPAnnotation(String, String) - Constructor for class umcg.genetica.ncbi.dbsnp.SNPAnnotation
SNPAnnotation(String, String, String) - Constructor for class umcg.genetica.ncbi.dbsnp.SNPAnnotation
SNPCHR - Static variable in class umcg.genetica.io.trityper.QTLTextFile
SNPLoader - Class in umcg.genetica.io.trityper
SNPLoader(RandomAccessFile, Boolean[], Boolean[]) - Constructor for class umcg.genetica.io.trityper.SNPLoader
SNPLoader(RandomAccessFile, RandomAccessFile, Boolean[], Boolean[]) - Constructor for class umcg.genetica.io.trityper.SNPLoader
SNPLOC - Static variable in class umcg.genetica.io.trityper.QTLTextFile
SNPTYPE - Static variable in class umcg.genetica.io.trityper.QTLTextFile
SoftfileAnnotation - Class in umcg.genetica.methylation
SoftfileAnnotation() - Constructor for class umcg.genetica.methylation.SoftfileAnnotation
sort() - Method in class umcg.genetica.io.ucsc.UCSCTrack
sort(E[]) - Static method in class umcg.genetica.util.InplaceArrayQuickSort
sort(E[], int, int) - Static method in class umcg.genetica.util.InplaceArrayQuickSort
sort(C[]) - Static method in class umcg.genetica.util.SmoothSort
sort(C[], int, int) - Static method in class umcg.genetica.util.SmoothSort
sort(Vector) - Method in class umcg.genetica.util.VectorSorter: Sort the given vector.
SortableSNP - Class in umcg.genetica.containers
SortableSNP(String, int, byte, int, SortableSNP.SORTBY) - Constructor for class umcg.genetica.containers.SortableSNP
SortableSNP(String, int, byte, int, double, SortableSNP.SORTBY) - Constructor for class umcg.genetica.containers.SortableSNP
SortableSNP.SORTBY - Enum in umcg.genetica.containers
sortGenePointers() - Method in class umcg.genetica.io.binInteraction.gene.BinaryInteractionGeneCreator
sortGenePointers() - Method in class umcg.genetica.io.binInteraction.variant.BinaryInteractionVariantCreator
SPACE - Static variable in class umcg.genetica.console.ConsoleGUIElems
space - Static variable in class umcg.genetica.io.text.TextFile
space - Static variable in class umcg.genetica.text.Strings
split(String) - Static method in class umcg.genetica.text.Strings
splitDosageInformationPerChromosome(String, String, String, String, String) - Method in class umcg.genetica.io.trityper.converters.TriTyperToPlinkDosage
square(double) - Static method in class umcg.genetica.math.Fmath
square(float) - Static method in class umcg.genetica.math.Fmath
square(BigDecimal) - Static method in class umcg.genetica.math.Fmath
square(int) - Static method in class umcg.genetica.math.Fmath
square(long) - Static method in class umcg.genetica.math.Fmath
square(BigInteger) - Static method in class umcg.genetica.math.Fmath
squareRootElements(double[]) - Static method in class umcg.genetica.math.Fmath
squareRootElements(float[]) - Static method in class umcg.genetica.math.Fmath
standardNormalize(double[]) - Static method in class umcg.genetica.math.stats.Normalization
standardNormalizeData() - Method in class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
start() - Method in class umcg.genetica.util.RunTimer
stop() - Method in class umcg.genetica.util.RunTimer
StringDoubleObject - Class in umcg.genetica.containers
StringDoubleObject(String, double) - Constructor for class umcg.genetica.containers.StringDoubleObject
StringDoubleObjectSorterSortOnDouble - Class in umcg.genetica.util
StringDoubleObjectSorterSortOnDouble() - Constructor for class umcg.genetica.util.StringDoubleObjectSorterSortOnDouble: Creates a new instance of GeneLocationObjectSorter
StringIntegerObject - Class in umcg.genetica.containers
StringIntegerObject(String, int) - Constructor for class umcg.genetica.containers.StringIntegerObject
StringIntegerObjectSorterSortOnInteger - Class in umcg.genetica.util
StringIntegerObjectSorterSortOnInteger() - Constructor for class umcg.genetica.util.StringIntegerObjectSorterSortOnInteger: Creates a new instance of GeneLocationObjectSorter
StringRange - Class in umcg.genetica.collections.intervaltree
StringRange(int, int, String) - Constructor for class umcg.genetica.collections.intervaltree.StringRange
Strings - Class in umcg.genetica.text
Strings() - Constructor for class umcg.genetica.text.Strings
stringValue - Variable in class umcg.genetica.containers.StringDoubleObject
stringValue - Variable in class umcg.genetica.containers.StringIntegerObject
sum(double[]) - Static method in class umcg.genetica.math.stats.Descriptives
supress() - Static method in class umcg.genetica.math.interpolation.CubicSpline
swapper - Variable in class umcg.genetica.util.RankArray
swapper - Variable in class umcg.genetica.util.RankDoubleArray
swapper - Variable in class umcg.genetica.util.RankIntArray
swapperdouble - Variable in class umcg.genetica.util.RankArray
SymmetricByteDistanceMatrix - Class in umcg.genetica.math.matrix: Symmetric Byte Distance Matrix: A memory efficient matrix capable of performing calculations on all genes x all genes:
SymmetricByteDistanceMatrix(int) - Constructor for class umcg.genetica.math.matrix.SymmetricByteDistanceMatrix: Creates a new instance of SymmetricByteDistancaMatrix Defines a new Symmetric matrix, with a predefined size Initially all values will be Byte.MAX_Value (127) All data is stored in memory efficient one dimensional array, which costs size * (size + 1) / 2 bytes
SymmetricByteDistanceMatrix(int, boolean) - Constructor for class umcg.genetica.math.matrix.SymmetricByteDistanceMatrix
SymmetricShortDistanceMatrix - Class in umcg.genetica.math.matrix: Symmetric Short Distance Matrix: A memory efficient matrix capable of performing calculations on all genes x all genes:
SymmetricShortDistanceMatrix(int) - Constructor for class umcg.genetica.math.matrix.SymmetricShortDistanceMatrix: Creates a new instance of SymmetricShortDistancaMatrix Defines a new Symmetric matrix, with a predefined size Initially all values will be Short.MAX_Value (65535) All data is stored in memory efficient one dimensional array, which costs size * (size + 1) bytes
SymmetricShortDistanceMatrix(int, boolean) - Constructor for class umcg.genetica.math.matrix.SymmetricShortDistanceMatrix

T

T - Static variable in class umcg.genetica.io.trityper.util.BaseAnnot
T_ABS - Static variable in class umcg.genetica.math.Fmath
TAB - Static variable in class umcg.genetica.console.ConsoleGUIElems
tab - Static variable in class umcg.genetica.io.text.TextFile
tab - Static variable in class umcg.genetica.text.Strings
tan(double, double, double, double, double, double) - Static method in class umcg.genetica.math.Fmath
tan(double, double, double) - Static method in class umcg.genetica.math.Fmath
tan(double) - Static method in class umcg.genetica.math.Fmath
tanh(double) - Static method in class umcg.genetica.math.Fmath
test(double[], double[]) - Static method in class umcg.genetica.math.stats.TTest: Calculate t-test two-sided P-value
testBlocks(String) - Static method in class umcg.genetica.io.bin.RandomAccessFile: Test the block operations of the RandomAccessFile class.
testBytes(String, int) - Static method in class umcg.genetica.io.bin.RandomAccessFile: Test the byte operations of the RandomAccessFile class.
TestGffIntervalTree - Class in umcg.genetica.io.gtf
TestGffIntervalTree() - Constructor for class umcg.genetica.io.gtf.TestGffIntervalTree
testZscore(double[], double[]) - Static method in class umcg.genetica.math.stats.TTest: Calculate t-test Z-score
TextFile - Class in umcg.genetica.io.text
TextFile(String, boolean) - Constructor for class umcg.genetica.io.text.TextFile
TextFile(File, boolean) - Constructor for class umcg.genetica.io.text.TextFile
TextFile(File, boolean, int) - Constructor for class umcg.genetica.io.text.TextFile
TextFile(String, boolean, int) - Constructor for class umcg.genetica.io.text.TextFile
TheilSen - Class in umcg.genetica.math.stats
toByte(String) - Static method in class umcg.genetica.io.trityper.util.BaseAnnot
toByteArray(String) - Static method in class umcg.genetica.io.trityper.util.BaseAnnot
tonToKg(double) - Static method in class umcg.genetica.math.Fmath
toPrimitiveArr(Double[]) - Static method in class umcg.genetica.util.Primitives
toString() - Method in class umcg.genetica.collections.intervaltree.StringRange
toString() - Method in class umcg.genetica.containers.Pair
toString() - Method in class umcg.genetica.containers.Triple
toString() - Method in class umcg.genetica.io.bin.RandomAccessFile: Create a string representation of this object.
toString() - Method in class umcg.genetica.io.gtf.GffElement
toString() - Method in class umcg.genetica.io.gwascatalog.GWASSNP
toString() - Method in class umcg.genetica.io.gwascatalog.GWASTrait
toString() - Method in class umcg.genetica.io.trityper.EQTL
toString(byte) - Static method in class umcg.genetica.io.trityper.util.BaseAnnot
toString() - Method in class umcg.genetica.io.ucsc.UCSCDataObject
transAnalysis - Variable in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDatasetSettings
Transcript - Class in umcg.genetica.containers
Transcript() - Constructor for class umcg.genetica.containers.Transcript
transformMToBetavalue(DoubleMatrix2D) - Static method in class umcg.genetica.methylation.ConvertBetaAndMvalues
transformMToBetavalue(double[][]) - Static method in class umcg.genetica.methylation.ConvertBetaAndMvalues
transformToMvalue(double[][]) - Static method in class umcg.genetica.methylation.ConvertBetaAndMvalues
transposeDataset() - Method in class umcg.genetica.math.matrix.DoubleMatrixDataset: Deprecated.
Triple<L,M,R> - Class in umcg.genetica.containers
Triple(L, M, R) - Constructor for class umcg.genetica.containers.Triple
TriTyperConcatDatasets - Class in umcg.genetica.io.trityper.util: This class can be used to concatenate several trityper datasets.
TriTyperConcatDatasets(String) - Constructor for class umcg.genetica.io.trityper.util.TriTyperConcatDatasets
TriTyperExpressionData - Class in umcg.genetica.io.trityper
TriTyperExpressionData() - Constructor for class umcg.genetica.io.trityper.TriTyperExpressionData
TriTyperExpressionData(String, String, String, boolean) - Constructor for class umcg.genetica.io.trityper.TriTyperExpressionData
TriTyperGeneticalGenomicsDataset - Class in umcg.genetica.io.trityper
TriTyperGeneticalGenomicsDataset(TriTyperGeneticalGenomicsDatasetSettings, Pair<List<String>, List<List<String>>>) - Constructor for class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDataset
TriTyperGeneticalGenomicsDataset(TriTyperGeneticalGenomicsDatasetSettings) - Constructor for class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDataset
TriTyperGeneticalGenomicsDatasetSettings - Class in umcg.genetica.io.trityper
TriTyperGeneticalGenomicsDatasetSettings() - Constructor for class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDatasetSettings
TriTyperGenotypeData - Class in umcg.genetica.io.trityper
TriTyperGenotypeData(String) - Constructor for class umcg.genetica.io.trityper.TriTyperGenotypeData
TriTyperGenotypeData() - Constructor for class umcg.genetica.io.trityper.TriTyperGenotypeData
TriTyperGenotypeDataMerger - Class in umcg.genetica.io.trityper.util
TriTyperGenotypeDataMerger() - Constructor for class umcg.genetica.io.trityper.util.TriTyperGenotypeDataMerger
TriTyperReferenceConcordantPedAndMapExporter - Class in umcg.genetica.io.trityper.converters
TriTyperReferenceConcordantPedAndMapExporter() - Constructor for class umcg.genetica.io.trityper.converters.TriTyperReferenceConcordantPedAndMapExporter
TriTyperSNPMappings - Class in umcg.genetica.io.trityper
TriTyperSNPMappings(String) - Constructor for class umcg.genetica.io.trityper.TriTyperSNPMappings
TriTyperSNPMappings(String, String) - Constructor for class umcg.genetica.io.trityper.TriTyperSNPMappings
TriTyperSNPMappings(String, Set<String>) - Constructor for class umcg.genetica.io.trityper.TriTyperSNPMappings
TriTyperToDosageConverter - Class in umcg.genetica.io.trityper.converters
TriTyperToDosageConverter() - Constructor for class umcg.genetica.io.trityper.converters.TriTyperToDosageConverter
TriTyperToMachImputedTransposed - Class in umcg.genetica.io.trityper.converters
TriTyperToMachImputedTransposed() - Constructor for class umcg.genetica.io.trityper.converters.TriTyperToMachImputedTransposed
TriTyperToPedAndMapConverter - Class in umcg.genetica.io.trityper.converters
TriTyperToPedAndMapConverter() - Constructor for class umcg.genetica.io.trityper.converters.TriTyperToPedAndMapConverter
TriTyperToPlinkDosage - Class in umcg.genetica.io.trityper.converters
TriTyperToPlinkDosage() - Constructor for class umcg.genetica.io.trityper.converters.TriTyperToPlinkDosage
TriTyperToTabSeparated - Class in umcg.genetica.io.trityper.converters
TriTyperToTabSeparated() - Constructor for class umcg.genetica.io.trityper.converters.TriTyperToTabSeparated
TriTyperToVCF - Class in umcg.genetica.io.trityper.converters
TriTyperToVCF() - Constructor for class umcg.genetica.io.trityper.converters.TriTyperToVCF
truncate(double, int) - Static method in class umcg.genetica.math.Fmath
truncate(float, int) - Static method in class umcg.genetica.math.Fmath
tsls(double[], double[], double[]) - Static method in class umcg.genetica.math.stats.TwoStepLeastSquares
tsls(double[], double[], double[], boolean) - Static method in class umcg.genetica.math.stats.TwoStepLeastSquares
tsProbesConfine - Variable in class umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDatasetSettings
TTest - Class in umcg.genetica.math.stats
TTest() - Constructor for class umcg.genetica.math.stats.TTest
TwoStepLeastSquares - Class in umcg.genetica.math.stats
TwoStepLeastSquares() - Constructor for class umcg.genetica.math.stats.TwoStepLeastSquares

U

U - Static variable in class umcg.genetica.io.trityper.util.BaseAnnot
UCSCDataObject - Class in umcg.genetica.io.ucsc
UCSCDataObject(byte, int, int, double, UCSCDataObject.SORTBY) - Constructor for class umcg.genetica.io.ucsc.UCSCDataObject
UCSCDataObject.SORTBY - Enum in umcg.genetica.io.ucsc
UCSCTrack - Class in umcg.genetica.io.ucsc
UCSCTrack(String) - Constructor for class umcg.genetica.io.ucsc.UCSCTrack
umcg.genetica.collections - package umcg.genetica.collections
umcg.genetica.collections.intervaltree - package umcg.genetica.collections.intervaltree
umcg.genetica.console - package umcg.genetica.console
umcg.genetica.containers - package umcg.genetica.containers
umcg.genetica.ensembl - package umcg.genetica.ensembl
umcg.genetica.genomicboundaries - package umcg.genetica.genomicboundaries
umcg.genetica.graphics - package umcg.genetica.graphics
umcg.genetica.gwas - package umcg.genetica.gwas
umcg.genetica.io - package umcg.genetica.io
umcg.genetica.io.bed - package umcg.genetica.io.bed
umcg.genetica.io.bedgraph - package umcg.genetica.io.bedgraph
umcg.genetica.io.bin - package umcg.genetica.io.bin
umcg.genetica.io.binInteraction - package umcg.genetica.io.binInteraction
umcg.genetica.io.binInteraction.gene - package umcg.genetica.io.binInteraction.gene
umcg.genetica.io.binInteraction.variant - package umcg.genetica.io.binInteraction.variant
umcg.genetica.io.concurrent - package umcg.genetica.io.concurrent
umcg.genetica.io.fasta - package umcg.genetica.io.fasta
umcg.genetica.io.geofiles - package umcg.genetica.io.geofiles
umcg.genetica.io.gmt - package umcg.genetica.io.gmt
umcg.genetica.io.gtf - package umcg.genetica.io.gtf
umcg.genetica.io.gwascatalog - package umcg.genetica.io.gwascatalog
umcg.genetica.io.pileup - package umcg.genetica.io.pileup
umcg.genetica.io.probemapping - package umcg.genetica.io.probemapping
umcg.genetica.io.regulomedb - package umcg.genetica.io.regulomedb
umcg.genetica.io.text - package umcg.genetica.io.text
umcg.genetica.io.text.converters - package umcg.genetica.io.text.converters
umcg.genetica.io.trityper - package umcg.genetica.io.trityper
umcg.genetica.io.trityper.bin - package umcg.genetica.io.trityper.bin
umcg.genetica.io.trityper.converters - package umcg.genetica.io.trityper.converters
umcg.genetica.io.trityper.probeannotation - package umcg.genetica.io.trityper.probeannotation
umcg.genetica.io.trityper.util - package umcg.genetica.io.trityper.util
umcg.genetica.io.ucsc - package umcg.genetica.io.ucsc
umcg.genetica.legacy - package umcg.genetica.legacy
umcg.genetica.math - package umcg.genetica.math
umcg.genetica.math.interpolation - package umcg.genetica.math.interpolation
umcg.genetica.math.matrix - package umcg.genetica.math.matrix
umcg.genetica.math.matrix2 - package umcg.genetica.math.matrix2
umcg.genetica.math.stats - package umcg.genetica.math.stats
umcg.genetica.math.stats.concurrent - package umcg.genetica.math.stats.concurrent
umcg.genetica.methylation - package umcg.genetica.methylation
umcg.genetica.ncbi.dbsnp - package umcg.genetica.ncbi.dbsnp
umcg.genetica.text - package umcg.genetica.text
umcg.genetica.text.parsing - package umcg.genetica.text.parsing
umcg.genetica.util - package umcg.genetica.util
umcg.genetica.variantAnnotator - package umcg.genetica.variantAnnotator
unread() - Method in class umcg.genetica.io.bin.RandomAccessFile: Unread the last byte read.
unsupress() - Static method in class umcg.genetica.math.interpolation.CubicSpline

V

valueOf(String) - Static method in enum umcg.genetica.containers.Pair.SORTBY: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umcg.genetica.containers.SortableSNP.SORTBY: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umcg.genetica.graphics.ForestPlot.Output: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umcg.genetica.graphics.Heatmap.Output: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umcg.genetica.graphics.ScatterPlot.OUTPUTFORMAT: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umcg.genetica.graphics.ViolinBoxPlot.Output: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umcg.genetica.io.ucsc.PeakFile.PEAKFORMAT: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umcg.genetica.io.ucsc.UCSCDataObject.SORTBY: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umcg.genetica.io.ucsc.WigFile.STEPMODE: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umcg.genetica.math.matrix.DoubleMatrixDatasetAC.LoadLabels: Deprecated.

Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umcg.genetica.math.stats.AndersonDarling.IS_DATA_NORMALIZED: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umcg.genetica.math.stats.FDRUtils.AbsoluteValues: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umcg.genetica.math.stats.FDRUtils.CloneArrays: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umcg.genetica.math.stats.FDRUtils.SortArrays: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umcg.genetica.math.stats.QValues.SMOOTHER: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umcg.genetica.util.RunTimer.Granularity: Returns the enum constant of this type with the specified name.
values() - Static method in enum umcg.genetica.containers.Pair.SORTBY: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umcg.genetica.containers.SortableSNP.SORTBY: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umcg.genetica.graphics.ForestPlot.Output: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umcg.genetica.graphics.Heatmap.Output: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umcg.genetica.graphics.ScatterPlot.OUTPUTFORMAT: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umcg.genetica.graphics.ViolinBoxPlot.Output: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umcg.genetica.io.ucsc.PeakFile.PEAKFORMAT: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umcg.genetica.io.ucsc.UCSCDataObject.SORTBY: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umcg.genetica.io.ucsc.WigFile.STEPMODE: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umcg.genetica.math.matrix.DoubleMatrixDatasetAC.LoadLabels: Deprecated.

Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umcg.genetica.math.stats.AndersonDarling.IS_DATA_NORMALIZED: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umcg.genetica.math.stats.FDRUtils.AbsoluteValues: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umcg.genetica.math.stats.FDRUtils.CloneArrays: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umcg.genetica.math.stats.FDRUtils.SortArrays: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umcg.genetica.math.stats.QValues.SMOOTHER: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umcg.genetica.util.RunTimer.Granularity: Returns an array containing the constants of this enum type, in the order they are declared.
variance(float[], double) - Static method in class umcg.genetica.math.stats.Descriptives: Calculate the variance for an array of floats
variance(double[]) - Static method in class umcg.genetica.math.stats.Descriptives
variance(double[], double) - Static method in class umcg.genetica.math.stats.Descriptives
VariantAnnotator<E extends GenomicRange> - Class in umcg.genetica.variantAnnotator
VariantAnnotator() - Constructor for class umcg.genetica.variantAnnotator.VariantAnnotator
VCFToTriTyper - Class in umcg.genetica.io.trityper.converters
VCFToTriTyper() - Constructor for class umcg.genetica.io.trityper.converters.VCFToTriTyper
VectorSorter - Class in umcg.genetica.util
VectorSorter() - Constructor for class umcg.genetica.util.VectorSorter: A default constructor.
VennDiagram - Class in umcg.genetica.graphics
VennDiagram(int) - Constructor for class umcg.genetica.graphics.VennDiagram
vers(double) - Static method in class umcg.genetica.math.Fmath
viewDice() - Method in class umcg.genetica.math.matrix2.DoubleMatrixDataset
ViolinBoxPlot - Class in umcg.genetica.graphics
ViolinBoxPlot() - Constructor for class umcg.genetica.graphics.ViolinBoxPlot
ViolinBoxPlot.Output - Enum in umcg.genetica.graphics

W

W - Static variable in class umcg.genetica.io.bin.BinaryFile
W - Static variable in class umcg.genetica.io.text.TextFile
W - Static variable in class umcg.genetica.io.trityper.bin.BinaryGZipFloatMatrix
W - Static variable in class umcg.genetica.io.trityper.bin.BinaryResultProbeSummary
W - Static variable in class umcg.genetica.io.trityper.bin.BinaryResultSNPSummary
WGAFileMatrixGenotype - Class in umcg.genetica.io.trityper
WGAFileMatrixGenotype(int, int, File, boolean) - Constructor for class umcg.genetica.io.trityper.WGAFileMatrixGenotype: Creates a new instance of WGAFileMatrixGenotype
WGAFileMatrixImputedDosage - Class in umcg.genetica.io.trityper
WGAFileMatrixImputedDosage(int, int, File, boolean) - Constructor for class umcg.genetica.io.trityper.WGAFileMatrixImputedDosage: Creates a new instance of WGAFileMatrixGenotype
WGAFileMatrixRawData - Class in umcg.genetica.io.trityper
WGAFileMatrixRawData(int, int, File, boolean) - Constructor for class umcg.genetica.io.trityper.WGAFileMatrixRawData: Creates a new instance of WGAFileMatrixRawData
whitespace - Static variable in class umcg.genetica.text.Strings
WigFile - Class in umcg.genetica.io.ucsc
WigFile(String, boolean) - Constructor for class umcg.genetica.io.ucsc.WigFile
WigFile.STEPMODE - Enum in umcg.genetica.io.ucsc
WilcoxonMannWhitney - Class in umcg.genetica.math.stats
WilcoxonMannWhitney() - Constructor for class umcg.genetica.math.stats.WilcoxonMannWhitney: Creates a new instance of WilcoxonMannWhitney
write(int) - Method in class com.mastfrog.util.streams.HashingOutputStream
write(int) - Method in class umcg.genetica.io.bin.BinaryFile
WRITE - Static variable in class umcg.genetica.io.bin.RandomAccessFile: Write to the file.
write(int) - Method in class umcg.genetica.io.bin.RandomAccessFile: Write a byte to the file.
write(byte[]) - Method in class umcg.genetica.io.bin.RandomAccessFile: Writes b.length bytes from the specified byte array starting at offset off to this file.
write(byte[], int, int) - Method in class umcg.genetica.io.bin.RandomAccessFile: Writes len bytes from the specified byte array starting at offset off to this file.
write(String) - Method in class umcg.genetica.io.text.TextFile
write(Float[]) - Method in class umcg.genetica.io.trityper.bin.BinaryGZipFloatMatrix
write(byte[]) - Method in class umcg.genetica.io.trityper.bin.BinaryGZipFloatMatrix
write(String[], Integer[][], TriTyperGeneticalGenomicsDataset[]) - Method in class umcg.genetica.io.trityper.bin.BinaryResultProbeSummary
write(String[]) - Method in class umcg.genetica.io.trityper.bin.BinaryResultProbeSummary
write(String, byte, Integer, double, double, double, byte[], byte, byte, Integer, long) - Method in class umcg.genetica.io.trityper.bin.BinaryResultSNPSummary
write(EQTL[]) - Method in class umcg.genetica.io.trityper.QTLTextFile
write(ArrayList<EQTL>) - Method in class umcg.genetica.io.trityper.QTLTextFile
writeable - Variable in class umcg.genetica.io.bin.BinaryFile
writeable - Variable in class umcg.genetica.io.text.TextFile
writeBool(boolean) - Method in class umcg.genetica.io.bin.BinaryFile
writeBoolean(boolean) - Method in class umcg.genetica.io.bin.RandomAccessFile: Writes a boolean to the file as a 1-byte value.
writeBoundariesToBedFile(String, String) - Method in class umcg.genetica.genomicboundaries.GenomicBoundaries: Write the data of the Boundary objects to a BED file, specified by @param bedFilePath.
writeByte(byte) - Method in class umcg.genetica.io.bin.BinaryFile
writeByte(int) - Method in class umcg.genetica.io.bin.RandomAccessFile: Writes a byte to the file as a 1-byte value.
writeBytes(byte[]) - Method in class umcg.genetica.io.bin.BinaryFile
writeBytes(byte[], int, int) - Method in class umcg.genetica.io.bin.RandomAccessFile: Write len bytes from an array to the file.
writeBytes(String) - Method in class umcg.genetica.io.bin.RandomAccessFile: Writes the string to the file as a sequence of bytes.
writeBytes(char[], int, int) - Method in class umcg.genetica.io.bin.RandomAccessFile: Writes the character array to the file as a sequence of bytes.
writeChar(int) - Method in class umcg.genetica.io.bin.RandomAccessFile: Writes a char to the file as a 2-byte value, high byte first.
writeChars(String) - Method in class umcg.genetica.io.bin.RandomAccessFile: Writes a string to the file as a sequence of characters.
writeConcatedDataset() - Method in class umcg.genetica.io.trityper.util.TriTyperConcatDatasets
writeDeflated(byte[]) - Method in class umcg.genetica.io.trityper.bin.BinaryGZipFloatMatrix
writeDouble(double) - Method in class umcg.genetica.io.bin.BinaryFile
writeDouble(double) - Method in class umcg.genetica.io.bin.RandomAccessFile: Converts the double argument to a long using the doubleToLongBits method in class Double, and then writes that long value to the file as an 8-byte quantity, high byte first.
writeFloat(float) - Method in class umcg.genetica.io.bin.BinaryFile
writeFloat(float) - Method in class umcg.genetica.io.bin.RandomAccessFile: Converts the float argument to an int using the floatToIntBits method in class Float, and then writes that int value to the file as a 4-byte quantity, high byte first.
writeGMTFileBasedOnGeneSetFileAndMappingFileRemovingDuplicateGeneSets(String, String, String, String) - Static method in class umcg.genetica.io.text.converters.NetworkConverter
writeInt(int) - Method in class umcg.genetica.io.bin.BinaryFile
writeInt(int) - Method in class umcg.genetica.io.bin.RandomAccessFile: Writes an int to the file as four bytes, high byte first.
writeList(List) - Method in class umcg.genetica.io.text.TextFile
writeln(CharSequence) - Method in class umcg.genetica.io.text.TextFile
writeln(String) - Method in class umcg.genetica.io.text.TextFile
writeln() - Method in class umcg.genetica.io.text.TextFile
writelnDelimited(Object[], Pattern) - Method in class umcg.genetica.io.text.TextFile
writelnsynced(String) - Method in class umcg.genetica.io.text.TextFile
writelnTabDelimited(Object[]) - Method in class umcg.genetica.io.text.TextFile
writeLong(long) - Method in class umcg.genetica.io.bin.BinaryFile
writeLong(long) - Method in class umcg.genetica.io.bin.RandomAccessFile: Writes a long to the file as eight bytes, high byte first.
writeShort(int) - Method in class umcg.genetica.io.bin.RandomAccessFile: Writes a short to the file as two bytes, high byte first.
writeString(String) - Method in class umcg.genetica.io.bin.BinaryFile
writeUTF(String) - Method in class umcg.genetica.io.bin.RandomAccessFile: Writes a string to the file using UTF-8 encoding in a machine-independent manner.

X

x - Variable in class umcg.genetica.util.RankArray
x - Variable in class umcg.genetica.util.RankDoubleArray
x - Variable in class umcg.genetica.util.RankIntArray
xdouble - Variable in class umcg.genetica.util.RankArray

Y

y - Variable in class umcg.genetica.util.RankArray
y - Variable in class umcg.genetica.util.RankDoubleArray
y - Variable in class umcg.genetica.util.RankIntArray
yardToMetre(double) - Static method in class umcg.genetica.math.Fmath
ydouble - Variable in class umcg.genetica.util.RankArray

Z

zero(int) - Static method in class umcg.genetica.math.interpolation.CubicSpline
zScore(double, double, double) - Static method in class umcg.genetica.math.stats.Descriptives
ZScores - Class in umcg.genetica.math.stats
ZScores() - Constructor for class umcg.genetica.math.stats.ZScores
zScoreToCorrelation(double, int) - Static method in class umcg.genetica.math.stats.ZScores
zToP(double) - Static method in class umcg.genetica.math.stats.FDRUtils: Returns the p-value corresponding to the given Z-score assuming a two tailed-test.
zToP(double) - Static method in class umcg.genetica.math.stats.KolmogorovSmirnov: Converts a Kolmogorov-Smirnov Z value to a p-value.
zToP(double) - Static method in class umcg.genetica.math.stats.ZScores: Returns the p-value corresponding to the given Z-score assuming a two tailed-test.

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z