umcg.genetica.math.matrix2

Class MatrixHandling

java.lang.Object

umcg.genetica.math.matrix2.MatrixHandling

public class MatrixHandling
extends Object

Author:

MarcJan

Constructor Summary

Constructors

Constructor and Description
MatrixHandling()

Method Summary

Modifier and Type	Method and Description
static void	appendPrefixToColnames(DoubleMatrixDataset<String,String> in, String prefix) Append a static prefix to the column names
static DoubleMatrixDataset<String,String>	CreatSubsetBasedOnColumns(DoubleMatrixDataset<String,String> dataset, HashSet<String> colNames, boolean remove) Filter out columns.
static DoubleMatrixDataset<String,String>	CreatSubsetBasedOnRows(DoubleMatrixDataset<String,String> dataset, HashSet<String> rowNames, boolean removeRows) Remove or filter rows.
static void	fixLinkedHashes(LinkedHashMap<String,Integer> hashMap)
static DoubleMatrixDataset<String,String>	RemoveColumns(DoubleMatrixDataset<String,String> dataset, HashSet<String> samplesToBeRemoved) Remove samples on forehand
static void	RemoveColumnsWithToManyMissingValues(DoubleMatrixDataset<String,String> dataset, int maxMissingValuesPerColumn, double missingValue) Remove columns with to many missing values
static void	RemoveDuplicatesSamples(DoubleMatrixDataset<String,String> dataset) Remove identical samples, based on all expression values
static DoubleMatrixDataset<String,String>	RemoveProbes(DoubleMatrixDataset<String,String> dataset, HashSet<String> probesToBeRemoved) Remove probes without correct mapping known on forehand
DoubleMatrixDataset<String,String>	RemoveRows(DoubleMatrixDataset<String,String> dataset, HashSet<String> probesToBeRemoved) Remove rows without correct mapping known on forehand
static void	RemoveRowsWithToManyMissingValues(DoubleMatrixDataset<String,String> dataset, int maxMissingValuesPerRow, double missingValue) Remove rows with to many missing values
static DoubleMatrixDataset<String,String>	RemoveSamples(DoubleMatrixDataset<String,String> dataset, HashSet<String> samplesToBeRemoved) Remove samples on forehand
static void	RenameCols(DoubleMatrixDataset<?,String> dataset, HashMap<String,String> newNames)
static void	RenameRows(DoubleMatrixDataset<String,?> dataset, HashMap<String,String> mappedProbeList)
static void	ReplaceMissingValuesPerColumn(cern.colt.matrix.tdouble.DoubleMatrix2D rawData, boolean useMedian, double NaValue) Replace missing values in the double matrix per sample.
static void	ReplaceMissingValuesPerRow(cern.colt.matrix.tdouble.DoubleMatrix2D rawData, boolean useMedian, double NaValue) Replace missing values in the double matrix per sample.
static void	ReplaceZerosToNull(cern.colt.matrix.tdouble.DoubleMatrix2D rawData) Replace zero's with nulls.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MatrixHandling

public MatrixHandling()

Method Detail

RemoveColumnsWithToManyMissingValues

public static void RemoveColumnsWithToManyMissingValues(DoubleMatrixDataset<String,String> dataset,
                                                        int maxMissingValuesPerColumn,
                                                        double missingValue)

Remove columns with to many missing values

Parameters:

dataset - DoubleMatrixDataset Expression matrix

hashColumnsToInclude - Ids of samples to include

missingValue, - missing value to check on. If not neccesary put to double.NaN

RemoveRowsWithToManyMissingValues

public static void RemoveRowsWithToManyMissingValues(DoubleMatrixDataset<String,String> dataset,
                                                     int maxMissingValuesPerRow,
                                                     double missingValue)

Remove rows with to many missing values

Parameters:

dataset - DoubleMatrixDataset Expression matrix

hashRowsToInclude - Ids of rowss to include

missingValue, - missing value to check on. If not neccesary put to double.NaN

RemoveDuplicatesSamples

public static void RemoveDuplicatesSamples(DoubleMatrixDataset<String,String> dataset)

Remove identical samples, based on all expression values

Parameters:

dataset - DoubleMatrixDataset Expression matrix

appendPrefixToColnames

public static void appendPrefixToColnames(DoubleMatrixDataset<String,String> in,
                                          String prefix)

Append a static prefix to the column names

Parameters:

in -

prefix -

ReplaceMissingValuesPerColumn

public static void ReplaceMissingValuesPerColumn(cern.colt.matrix.tdouble.DoubleMatrix2D rawData,
                                                 boolean useMedian,
                                                 double NaValue)

Replace missing values in the double matrix per sample. Using either the mean if useMedian is false or the median is useMedian is true.

Parameters:

rawData -

useMedian -

NaValue -

ReplaceMissingValuesPerRow

public static void ReplaceMissingValuesPerRow(cern.colt.matrix.tdouble.DoubleMatrix2D rawData,
                                              boolean useMedian,
                                              double NaValue)

Replace missing values in the double matrix per sample. Using either the mean if useMedian is false or the median is useMedian is true.

Parameters:

rawData -

useMedian -

NaValue -

RemoveProbes

public static DoubleMatrixDataset<String,String> RemoveProbes(DoubleMatrixDataset<String,String> dataset,
                                                              HashSet<String> probesToBeRemoved)

Remove probes without correct mapping known on forehand

Parameters:

dataset - DoubleMatrixDataset containing the matrix of interest

probesToBeRemoved - ArrayList with identifiers of probes that should be removed

fixLinkedHashes

public static void fixLinkedHashes(LinkedHashMap<String,Integer> hashMap)

RenameRows

public static void RenameRows(DoubleMatrixDataset<String,?> dataset,
                              HashMap<String,String> mappedProbeList)

RemoveRows

public DoubleMatrixDataset<String,String> RemoveRows(DoubleMatrixDataset<String,String> dataset,
                                                     HashSet<String> probesToBeRemoved)

Remove rows without correct mapping known on forehand

Parameters:

dataset - DoubleMatrixDataset containing the matrix of interest

probesToBeRemoved - ArrayList with identifiers of probes that should be removed

CreatSubsetBasedOnRows

public static DoubleMatrixDataset<String,String> CreatSubsetBasedOnRows(DoubleMatrixDataset<String,String> dataset,
                                                                        HashSet<String> rowNames,
                                                                        boolean removeRows)

Remove or filter rows.

Parameters:

dataset - DoubleMatrixDataset containing the matrix of interest

rowNames - ArrayList with identifiers of probes that

removeRows, - if true row ids in rowNames are removed if false rowNames are selected others are removed. should be removed

RemoveSamples

public static DoubleMatrixDataset<String,String> RemoveSamples(DoubleMatrixDataset<String,String> dataset,
                                                               HashSet<String> samplesToBeRemoved)

Remove samples on forehand

Parameters:

dataset - DoubleMatrixDataset containing the matrix of interest

samplesToBeRemoved - ArrayList with identifiers of probes that should be removed

RemoveColumns

public static DoubleMatrixDataset<String,String> RemoveColumns(DoubleMatrixDataset<String,String> dataset,
                                                               HashSet<String> samplesToBeRemoved)

Remove samples on forehand

Parameters:

dataset - DoubleMatrixDataset containing the matrix of interest

samplesToBeRemoved - ArrayList with identifiers of probes that should be removed

CreatSubsetBasedOnColumns

public static DoubleMatrixDataset<String,String> CreatSubsetBasedOnColumns(DoubleMatrixDataset<String,String> dataset,
                                                                           HashSet<String> colNames,
                                                                           boolean remove)

Filter out columns. Keep all columns that in in the hashset.

Parameters:

dataset -

colNames -

remove, - if true col ids in colNames are removed if false colNames are selected others are removed.

RenameCols

public static void RenameCols(DoubleMatrixDataset<?,String> dataset,
                              HashMap<String,String> newNames)

ReplaceZerosToNull

public static void ReplaceZerosToNull(cern.colt.matrix.tdouble.DoubleMatrix2D rawData)

Replace zero's with nulls.

Parameters:

rawData -