Uses of Class
umcg.genetica.math.matrix.DoubleMatrixDataset

Packages that use DoubleMatrixDataset

Package	Description
umcg.genetica.io.geofiles
umcg.genetica.io.probemapping
umcg.genetica.io.trityper
umcg.genetica.math.matrix
umcg.genetica.math.stats
umcg.genetica.methylation

Uses of DoubleMatrixDataset in umcg.genetica.io.geofiles

Methods in umcg.genetica.io.geofiles that return DoubleMatrixDataset

Modifier and Type	Method and Description
static DoubleMatrixDataset<String,String>	ParseSoftFile.importSOFTFile(String fileLocation, int numberOfSamples, int numberOfProbes)
static DoubleMatrixDataset<String,String>	ParseSoftFile.importSOFTFileSelection(String fileLocation, int numberOfSamples, int numberOfProbes, int samplesPerDataset)

Uses of DoubleMatrixDataset in umcg.genetica.io.probemapping

Methods in umcg.genetica.io.probemapping that return DoubleMatrixDataset

Modifier and Type	Method and Description
static DoubleMatrixDataset<String,String>	reading.readDoubleMatrixFile(String eigenVectorFile, Set<String> rowsToInclude) Read double matrix file restricting to given rows Eigenvector file / pc file / probe matrix

Uses of DoubleMatrixDataset in umcg.genetica.io.trityper

Methods in umcg.genetica.io.trityper that return DoubleMatrixDataset

Modifier and Type	Method and Description
DoubleMatrixDataset<String,String>	TriTyperGeneticalGenomicsDataset.getCovariateData()

Uses of DoubleMatrixDataset in umcg.genetica.math.matrix

Methods in umcg.genetica.math.matrix that return DoubleMatrixDataset

Modifier and Type	Method and Description
static DoubleMatrixDataset<String,String>	MergeDoubleMatrices.combineBasedOnCols(ArrayList<DoubleMatrixDataset> datasets) Merge a set of matrices based on column identifiers.
static DoubleMatrixDataset<String,String>	MergeDoubleMatrices.combineBasedOnRows(ArrayList<DoubleMatrixDataset> datasets) Merge a set of matrices based on row identifiers.
DoubleMatrixDataset<U,T>	DoubleMatrixDataset.getTransposedDataset() Deprecated.
static DoubleMatrixDataset<String,String>	MergeDoubleMatrices.mergeMatrixBasedOnColumns(DoubleMatrixDataset<String,String> matrixI, DoubleMatrixDataset<String,String> matrixII, boolean removeOldMatrix) Merge a matrix based on shared column identifiers.
static DoubleMatrixDataset<String,String>	MergeDoubleMatrices.mergeMatrixBasedOnRows(DoubleMatrixDataset<String,String> matrixI, DoubleMatrixDataset<String,String> matrixII, boolean removeOldMatrix) Merge a matrix based on row identifiers.

Methods in umcg.genetica.math.matrix with parameters of type DoubleMatrixDataset

Modifier and Type	Method and Description
static void	MatrixHandling.appendStringToColnames(DoubleMatrixDataset<String,String> in, String tissueSource)
static void	MatrixHandling.FilterCols(DoubleMatrixDataset<String,String> dataset, HashSet<String> keepCols)
static void	MatrixHandling.FilterRows(DoubleMatrixDataset<String,String> dataset, HashSet<String> probesToKeep) Remove rows without correct mapping known on forehand
static DoubleMatrixDataset<String,String>	MergeDoubleMatrices.mergeMatrixBasedOnColumns(DoubleMatrixDataset<String,String> matrixI, DoubleMatrixDataset<String,String> matrixII, boolean removeOldMatrix) Merge a matrix based on shared column identifiers.
static DoubleMatrixDataset<String,String>	MergeDoubleMatrices.mergeMatrixBasedOnColumns(DoubleMatrixDataset<String,String> matrixI, DoubleMatrixDataset<String,String> matrixII, boolean removeOldMatrix) Merge a matrix based on shared column identifiers.
static DoubleMatrixDataset<String,String>	MergeDoubleMatrices.mergeMatrixBasedOnRows(DoubleMatrixDataset<String,String> matrixI, DoubleMatrixDataset<String,String> matrixII, boolean removeOldMatrix) Merge a matrix based on row identifiers.
static DoubleMatrixDataset<String,String>	MergeDoubleMatrices.mergeMatrixBasedOnRows(DoubleMatrixDataset<String,String> matrixI, DoubleMatrixDataset<String,String> matrixII, boolean removeOldMatrix) Merge a matrix based on row identifiers.
static void	MatrixHandling.OrderOnColumns(DoubleMatrixDataset doubleMatrixDataset) Order columns
static void	MatrixHandling.OrderOnRows(DoubleMatrixDataset doubleMatrixDataset) Order rows
static void	MatrixHandling.performQC(DoubleMatrixDataset<String,String> dataset, ArrayList<String> probesToBeRemoved, ArrayList<String> samplesToBeRemoved, boolean replaceKnownOutOfRangeValues, int maxMissingSamplesMissingAProbe, int maxMissingProbesMissingPerSample) Method to apply all QC steps.
static void	MatrixHandling.RemoveColumns(DoubleMatrixDataset<String,String> dataset, HashSet<String> samplesToBeRemoved) Remove samples on forehand
static void	MatrixHandling.RemoveColumnsWithToManyMissingValues(DoubleMatrixDataset<String,String> dataset, int maxMissingValuesPerColumn) Remove columns with to many missing values
static void	MatrixHandling.RemoveDuplicateRowNames(DoubleMatrixDataset<String,String> dataset)
static void	MatrixHandling.RemoveDuplicatesSamples(DoubleMatrixDataset<String,String> dataset, boolean advanced) Remove identical samples, based on name and/or based on all expression value (advanced = true)
static void	MatrixHandling.RemoveProbes(DoubleMatrixDataset<String,String> dataset, HashSet<String> probesToBeRemoved) Remove probes without correct mapping known on forehand
static void	MatrixHandling.RemoveRows(DoubleMatrixDataset<String,String> dataset, HashSet<String> probesToBeRemoved) Remove rows without correct mapping known on forehand
static void	MatrixHandling.RemoveRowsWithToManyMissingValues(DoubleMatrixDataset<String,String> dataset, int maxMissingValuesPerRow) Remove rows with to many missing values
static void	MatrixHandling.RemoveSamples(DoubleMatrixDataset<String,String> dataset, HashSet<String> samplesToBeRemoved) Remove samples on forehand
static void	MatrixHandling.RenameCols(DoubleMatrixDataset<String,String> dataset, HashMap<String,String> newNames)
static void	MatrixHandling.ReorderRows(DoubleMatrixDataset<String,String> dataset, HashMap<String,Integer> mappingIndex) Order rows to a index

Method parameters in umcg.genetica.math.matrix with type arguments of type DoubleMatrixDataset

Modifier and Type	Method and Description
static DoubleMatrixDataset<String,String>	MergeDoubleMatrices.combineBasedOnCols(ArrayList<DoubleMatrixDataset> datasets) Merge a set of matrices based on column identifiers.
static DoubleMatrixDataset<String,String>	MergeDoubleMatrices.combineBasedOnRows(ArrayList<DoubleMatrixDataset> datasets) Merge a set of matrices based on row identifiers.

Uses of DoubleMatrixDataset in umcg.genetica.math.stats

Methods in umcg.genetica.math.stats with parameters of type DoubleMatrixDataset

Modifier and Type	Method and Description
static void	QuantileNormalization.QuantileNormAdressingNaValuesAfterInitialQN(DoubleMatrixDataset<String,String> dataset, boolean retainNA, boolean useRow, boolean keepZero) 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.

Uses of DoubleMatrixDataset in umcg.genetica.methylation

Methods in umcg.genetica.methylation that return DoubleMatrixDataset

Modifier and Type	Method and Description
static DoubleMatrixDataset<String,String>	ConverteUandMTo.Beta(DoubleMatrixDataset<String,String> uChanel, DoubleMatrixDataset<String,String> mChanel)
static DoubleMatrixDataset<String,String>	ConverteUandMTo.Mvalue(DoubleMatrixDataset<String,String> uChanel, DoubleMatrixDataset<String,String> mChanel)
static DoubleMatrixDataset<String,String>	ParseTcgaMethylationFile.parseTCGAData_lvl1(String fileInputFolder, boolean printToFile, String fileOutputFolder, boolean TcgaMethod) Read Level 1 data from TGCA a single DoubleMatrixDatasets containing beta values.
static DoubleMatrixDataset<String,String>	ParseTcgaMethylationFile.parseTCGAData_lvl3(String fileInputFolder, int nrProbes, boolean printToFile, String fileOut) Read level 3 data from TCGA Return DoubleMatrixDataset beta-values
static DoubleMatrixDataset<String,String>	ParseTcgaMethylationFile.parseTCGAData450As27K_lvl1(String fileInputFolder, boolean printToFile, String fileOutputFolder, boolean TcgaMethod, HashMap<String,Boolean> probeList) Read Level 1 450K data from TGCA a single DoubleMatrixDatasets containing beta values.

Methods in umcg.genetica.methylation that return types with arguments of type DoubleMatrixDataset

Modifier and Type	Method and Description
static ArrayList<DoubleMatrixDataset<String,String>>	ParseTcgaMethylationFile.parseTCGAData_lvl1_all_matrices(String fileInputFolder, boolean printToFile, String fileOutputFolder, boolean TcgaMethod) Read Level 1 data from TGCA Return 3 DoubleMatrixDatasets, methylated probe values, un-methylated probe values and beta values.

Methods in umcg.genetica.methylation with parameters of type DoubleMatrixDataset

Modifier and Type	Method and Description
static void	AssociatingPcasWithAnnotation.associateAnovaScoreAndItemOfInterest(DoubleMatrixDataset<String,String> doubleMatrix, HashMap<String,HashMap<String,String>> interestSets) Test for difference between all GSE groups with Anova.
static void	AssociatingPcasWithAnnotation.associateScoreAndItemOfInterest(DoubleMatrixDataset<String,String> doubleMatrix, HashMap<String,HashMap<String,String>> interestSets, ArrayList<String> entries) Test for difference between 2 groups with T-test.
static DoubleMatrixDataset<String,String>	ConverteUandMTo.Beta(DoubleMatrixDataset<String,String> uChanel, DoubleMatrixDataset<String,String> mChanel)
static DoubleMatrixDataset<String,String>	ConverteUandMTo.Beta(DoubleMatrixDataset<String,String> uChanel, DoubleMatrixDataset<String,String> mChanel)
static ArrayList<String>	CheckMatrixForValidBetaValues.checkMinAndMaxPerSample(DoubleMatrixDataset<String,String> dataset, boolean replaceCheckedValuesOutOfRange) Check if all probe values are actually between 0 and 1.
static void	AssociatingPcasWithAnnotation.correlateScoreAndItemOfInterest(DoubleMatrixDataset<String,String> doubleMatrix, HashMap<String,HashMap<String,String>> interestSets, String outfile, boolean samplesOnRows) Correlate values of interest to age
static DoubleMatrixDataset<String,String>	ConverteUandMTo.Mvalue(DoubleMatrixDataset<String,String> uChanel, DoubleMatrixDataset<String,String> mChanel)
static DoubleMatrixDataset<String,String>	ConverteUandMTo.Mvalue(DoubleMatrixDataset<String,String> uChanel, DoubleMatrixDataset<String,String> mChanel)