Uses of Class
umcg.genetica.math.matrix2.DoubleMatrixDataset

Packages that use DoubleMatrixDataset

Package	Description
umcg.genetica.io.geofiles
umcg.genetica.math.matrix2
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>	ParseTextTable.parseGeoTables(String fileInput, boolean debug) Geo text tables for HT12 v3 / v4 data

Uses of DoubleMatrixDataset in umcg.genetica.math.matrix2

Methods in umcg.genetica.math.matrix2 that return DoubleMatrixDataset

Modifier and Type	Method and Description
static DoubleMatrixDataset<String,String>	MergeDoubleMatrices.combineBasedOnCols(ArrayList<DoubleMatrixDataset<String,String>> datasets) Merge a set of matrices based on column identifiers.
static DoubleMatrixDataset<String,String>	MergeDoubleMatrices.combineBasedOnRows(ArrayList<DoubleMatrixDataset<String,String>> datasets) Merge a set of matrices based on row identifiers.
static DoubleMatrixDataset<String,String>	MatrixHandling.CreatSubsetBasedOnColumns(DoubleMatrixDataset<String,String> dataset, HashSet<String> colNames, boolean remove) Filter out columns.
static DoubleMatrixDataset<String,String>	MatrixHandling.CreatSubsetBasedOnRows(DoubleMatrixDataset<String,String> dataset, HashSet<String> rowNames, boolean removeRows) Remove or filter rows.
static DoubleMatrixDataset<String,String>	DoubleMatrixDataset.loadDoubleData(String fileName)
static DoubleMatrixDataset<String,String>	DoubleMatrixDataset.loadDoubleTextData(String fileName, String delimiter)
static DoubleMatrixDataset<String,String>	DoubleMatrixDataset.loadSubsetOfTextDoubleData(String fileName, String delimiter, HashSet<String> desiredRows, HashSet<String> desiredCols)
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>	MatrixHandling.RemoveColumns(DoubleMatrixDataset<String,String> dataset, HashSet<String> samplesToBeRemoved) Remove samples on forehand
static DoubleMatrixDataset<String,String>	MatrixHandling.RemoveProbes(DoubleMatrixDataset<String,String> dataset, HashSet<String> probesToBeRemoved) Remove probes without correct mapping known on forehand
DoubleMatrixDataset<String,String>	MatrixHandling.RemoveRows(DoubleMatrixDataset<String,String> dataset, HashSet<String> probesToBeRemoved) Remove rows without correct mapping known on forehand
static DoubleMatrixDataset<String,String>	MatrixHandling.RemoveSamples(DoubleMatrixDataset<String,String> dataset, HashSet<String> samplesToBeRemoved) Remove samples on forehand
DoubleMatrixDataset<C,R>	DoubleMatrixDataset.viewDice()

Methods in umcg.genetica.math.matrix2 with parameters of type DoubleMatrixDataset

Modifier and Type	Method and Description
static void	MatrixHandling.appendPrefixToColnames(DoubleMatrixDataset<String,String> in, String prefix) Append a static prefix to the column names
static DoubleMatrixDataset<String,String>	MatrixHandling.CreatSubsetBasedOnColumns(DoubleMatrixDataset<String,String> dataset, HashSet<String> colNames, boolean remove) Filter out columns.
static DoubleMatrixDataset<String,String>	MatrixHandling.CreatSubsetBasedOnRows(DoubleMatrixDataset<String,String> dataset, HashSet<String> rowNames, boolean removeRows) Remove or filter rows.
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 DoubleMatrixDataset<String,String>	MatrixHandling.RemoveColumns(DoubleMatrixDataset<String,String> dataset, HashSet<String> samplesToBeRemoved) Remove samples on forehand
static void	MatrixHandling.RemoveColumnsWithToManyMissingValues(DoubleMatrixDataset<String,String> dataset, int maxMissingValuesPerColumn, double missingValue) Remove columns with to many missing values
static void	MatrixHandling.RemoveDuplicatesSamples(DoubleMatrixDataset<String,String> dataset) Remove identical samples, based on all expression values
static DoubleMatrixDataset<String,String>	MatrixHandling.RemoveProbes(DoubleMatrixDataset<String,String> dataset, HashSet<String> probesToBeRemoved) Remove probes without correct mapping known on forehand
DoubleMatrixDataset<String,String>	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, double missingValue) Remove rows with to many missing values
static DoubleMatrixDataset<String,String>	MatrixHandling.RemoveSamples(DoubleMatrixDataset<String,String> dataset, HashSet<String> samplesToBeRemoved) Remove samples on forehand
static void	MatrixHandling.RenameCols(DoubleMatrixDataset<?,String> dataset, HashMap<String,String> newNames)
static void	MatrixHandling.RenameRows(DoubleMatrixDataset<String,?> dataset, HashMap<String,String> mappedProbeList)

Method parameters in umcg.genetica.math.matrix2 with type arguments of type DoubleMatrixDataset

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

Uses of DoubleMatrixDataset in umcg.genetica.methylation

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

Modifier and Type	Method and Description
static void	CheckMatrixForValidBetaValues.checkBetaValues(DoubleMatrixDataset<String,String> dataset, boolean replaceCheckedValuesOutOfRange) Check if all probe values are actually between 0 and 1.