umcg.genetica.math.matrix

Class MatrixHandling

java.lang.Object

umcg.genetica.math.matrix.MatrixHandling

public class MatrixHandling
extends Object

Author:

Marc Jan

Constructor Summary

Constructors

Constructor and Description
MatrixHandling()

Method Summary

Modifier and Type	Method and Description
static void	appendStringToColnames(DoubleMatrixDataset<String,String> in, String tissueSource)
static void	FilterCols(DoubleMatrixDataset<String,String> dataset, HashSet<String> keepCols)
static void	FilterRows(DoubleMatrixDataset<String,String> dataset, HashSet<String> probesToKeep) Remove rows without correct mapping known on forehand
static void	OrderOnColumns(DoubleMatrixDataset doubleMatrixDataset) Order columns
static void	OrderOnRows(DoubleMatrixDataset doubleMatrixDataset) Order rows
static void	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	RemoveColumns(DoubleMatrixDataset<String,String> dataset, HashSet<String> samplesToBeRemoved) Remove samples on forehand
static void	RemoveColumnsWithToManyMissingValues(DoubleMatrixDataset<String,String> dataset, int maxMissingValuesPerColumn) Remove columns with to many missing values
static void	RemoveDuplicateRowNames(DoubleMatrixDataset<String,String> dataset)
static void	RemoveDuplicatesSamples(DoubleMatrixDataset<String,String> dataset, boolean advanced) Remove identical samples, based on name and/or based on all expression value (advanced = true)
static void	RemoveProbes(DoubleMatrixDataset<String,String> dataset, HashSet<String> probesToBeRemoved) Remove probes without correct mapping known on forehand
static void	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) Remove rows with to many missing values
static void	RemoveSamples(DoubleMatrixDataset<String,String> dataset, HashSet<String> samplesToBeRemoved) Remove samples on forehand
static void	RenameCols(DoubleMatrixDataset<String,String> dataset, HashMap<String,String> newNames)
static void	ReorderRows(DoubleMatrixDataset<String,String> dataset, HashMap<String,Integer> mappingIndex) Order rows to a index
static void	ReplaceMissingValues(double[][] rawData, boolean useMedian) Replace missing values in the double matrix per sample.
static void	ReplaceNullToZero(double[][] rawData) Replace null's with zero's.
static void	ReplaceZerosToNull(double[][] 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)

Remove columns with to many missing values

Parameters:

dataset - DoubleMatrixDataset Expression matrix

hashColumnsToInclude - Ids of samples to include

RemoveRowsWithToManyMissingValues

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

Remove rows with to many missing values

Parameters:

dataset - DoubleMatrixDataset Expression matrix

hashRowsToInclude - Ids of rowss to include

RemoveDuplicatesSamples

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

Remove identical samples, based on name and/or based on all expression value (advanced = true)

Parameters:

dataset - DoubleMatrixDataset Expression matrix

advanced - Do sample check based on double values

RemoveRows

public static void 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

FilterRows

public static void FilterRows(DoubleMatrixDataset<String,String> dataset,
                              HashSet<String> probesToKeep)

Remove rows without correct mapping known on forehand

Parameters:

dataset - DoubleMatrixDataset containing the matrix of interest

probesToKeep - ArrayList with identifiers of probes that should be removed

RemoveProbes

public static void 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

RemoveColumns

public static void 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

RemoveSamples

public static void 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

OrderOnRows

public static void OrderOnRows(DoubleMatrixDataset doubleMatrixDataset)

Order rows

Parameters:

dataset - DoubleMatrixDataset Expression matrix

OrderOnColumns

public static void OrderOnColumns(DoubleMatrixDataset doubleMatrixDataset)

Order columns

Parameters:

dataset - DoubleMatrixDataset Expression matrix

ReorderRows

public static void ReorderRows(DoubleMatrixDataset<String,String> dataset,
                               HashMap<String,Integer> mappingIndex)

Order rows to a index

Parameters:

dataset - DoubleMatrixDataset Expression matrix

hashRowsToInclude - Ids of rowss to include

ReplaceMissingValues

public static void ReplaceMissingValues(double[][] rawData,
                                        boolean useMedian)

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 -

ReplaceZerosToNull

public static void ReplaceZerosToNull(double[][] rawData)

Replace zero's with nulls.

Parameters:

rawData -

ReplaceNullToZero

public static void ReplaceNullToZero(double[][] rawData)

Replace null's with zero's.

Parameters:

rawData -

performQC

public static void performQC(DoubleMatrixDataset<String,String> dataset,
                             ArrayList<String> probesToBeRemoved,
                             ArrayList<String> samplesToBeRemoved,
                             boolean replaceKnownOutOfRangeValues,
                             int maxMissingSamplesMissingAProbe,
                             int maxMissingProbesMissingPerSample)

Method to apply all QC steps.

Parameters:

dataset -

probesToBeRemoved -

samplesToBeRemoved -

replaceKnownOutOfRangeValues -

maxMissingSamplesMissingAProbe -

maxMissingProbesMissingPerSample -

FilterCols

public static void FilterCols(DoubleMatrixDataset<String,String> dataset,
                              HashSet<String> keepCols)

RenameCols

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

appendStringToColnames

public static void appendStringToColnames(DoubleMatrixDataset<String,String> in,
                                          String tissueSource)

RemoveDuplicateRowNames

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