math_utils
Class ExpressionMatrix

java.lang.Object
  math_utils.ExpressionMatrix

public class ExpressionMatrix
extends java.lang.Object

This class implements and expression matrix object. It supports parsing of an expression matrix file and manipulations of the data.

Field Summary

java.util.ArrayList<java.lang.String>	genesID
float[][]	matrix

Constructor Summary

ExpressionMatrix(float[][] mat, java.lang.String[] h, java.util.ArrayList<java.lang.String> ids)

ExpressionMatrix(java.lang.String path)

Method Summary

void	addRowsToMatrix(ExpressionMatrix other)
boolean	containsGene(java.lang.String name)
void	createGene2IndexHash()
ExpressionMatrix	deepClone()
void	floorData(float val)
float	geneGenesCorrelations(java.lang.String first, java.lang.String second)
double[][]	getDoubleTrasposedMatrix()
ExpressionMatrix	getExpandedByGraph(short[][] graph)
java.util.ArrayList<java.lang.String>	getGenesID()
java.lang.String[]	getHeader()
float[][]	getMatrix()
ExpressionMatrix	getShuffeledMatrixByColumns(java.util.Random rand)
ExpressionMatrix	getSubMatrixByColumnsIndices(java.util.ArrayList<java.lang.Integer> list) This method receives a sorted list of indices and returns a sub-matrix that contains only the columns that are included in the list
ExpressionMatrix	getSubMatrixByRowsIndices(java.util.LinkedList<java.lang.Integer> list) This method returns a sub-matrix with all the raws that appear in the list.
java.util.LinkedList<java.lang.Integer>	intensityFilterGenes(float thr, float percentage, int[] borders)
java.util.LinkedList<java.lang.Integer>	intensityFilterGenesForOneClass(float thr, float percentage, int[] borders, int classIndex)
ExpressionMatrix	matrixByClusteringResults(java.util.LinkedList<java.util.LinkedList<java.lang.Integer>> clusteringResult) unite clusters into median pattern
void	printMatrix()
void	printMatrix(java.io.BufferedWriter writer)
void	printWekaCSVForRegression(java.lang.String path)
void	printWekaCSVInstancesArePatients(java.lang.String path, int[] borders, int classIndex) WEKA receives tab separated files, the header contains the features names and each line is an instance.
void	printWekaCSVInstancesArePatients(java.lang.String path, int[] borders, java.lang.String[] classesNames)
ExpressionMatrix	removeGenes(java.util.LinkedList<java.lang.Integer> toRemove)
void	setMatrix(float[][] matrix)
void	shuffleExpressions()
void	standardizeByClasses(int[] borders)

Methods inherited from class java.lang.Object

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

Field Detail

matrix

public float[][] matrix

genesID

public java.util.ArrayList<java.lang.String> genesID

Constructor Detail

ExpressionMatrix

public ExpressionMatrix(float[][] mat,
                        java.lang.String[] h,
                        java.util.ArrayList<java.lang.String> ids)

ExpressionMatrix

public ExpressionMatrix(java.lang.String path)

Method Detail

matrixByClusteringResults

public ExpressionMatrix matrixByClusteringResults(java.util.LinkedList<java.util.LinkedList<java.lang.Integer>> clusteringResult)

unite clusters into median pattern

Parameters:

clusteringResult -

Returns:

getSubMatrixByRowsIndices

public ExpressionMatrix getSubMatrixByRowsIndices(java.util.LinkedList<java.lang.Integer> list)

This method returns a sub-matrix with all the raws that appear in the list. The given parameter is an ArrayList of indices of raws in the matrix, in ascending order;

getSubMatrixByColumnsIndices

public ExpressionMatrix getSubMatrixByColumnsIndices(java.util.ArrayList<java.lang.Integer> list)

This method receives a sorted list of indices and returns a sub-matrix that contains only the columns that are included in the list

printWekaCSVInstancesArePatients

public void printWekaCSVInstancesArePatients(java.lang.String path,
                                             int[] borders,
                                             int classIndex)

WEKA receives tab separated files, the header contains the features names and each line is an instance. Therefore the expander matrix is the transpose of the WEKA's matrix. This method prints the transposed matrix. The last column in the output matrix is the class name, this is the default in WEKA.

Parameters:

writer -

printWekaCSVForRegression

public void printWekaCSVForRegression(java.lang.String path)

getDoubleTrasposedMatrix

public double[][] getDoubleTrasposedMatrix()

printWekaCSVInstancesArePatients

public void printWekaCSVInstancesArePatients(java.lang.String path,
                                             int[] borders,
                                             java.lang.String[] classesNames)

getMatrix

public float[][] getMatrix()

getHeader

public java.lang.String[] getHeader()

getGenesID

public java.util.ArrayList<java.lang.String> getGenesID()

containsGene

public boolean containsGene(java.lang.String name)

geneGenesCorrelations

public float geneGenesCorrelations(java.lang.String first,
                                   java.lang.String second)

createGene2IndexHash

public void createGene2IndexHash()

intensityFilterGenes

public java.util.LinkedList<java.lang.Integer> intensityFilterGenes(float thr,
                                                                    float percentage,
                                                                    int[] borders)

intensityFilterGenesForOneClass

public java.util.LinkedList<java.lang.Integer> intensityFilterGenesForOneClass(float thr,
                                                                               float percentage,
                                                                               int[] borders,
                                                                               int classIndex)

addRowsToMatrix

public void addRowsToMatrix(ExpressionMatrix other)

setMatrix

public void setMatrix(float[][] matrix)

floorData

public void floorData(float val)

printMatrix

public void printMatrix()

printMatrix

public void printMatrix(java.io.BufferedWriter writer)
                 throws java.io.IOException

Throws:

java.io.IOException

removeGenes

public ExpressionMatrix removeGenes(java.util.LinkedList<java.lang.Integer> toRemove)

getExpandedByGraph

public ExpressionMatrix getExpandedByGraph(short[][] graph)

standardizeByClasses

public void standardizeByClasses(int[] borders)

shuffleExpressions

public void shuffleExpressions()

deepClone

public ExpressionMatrix deepClone()

getShuffeledMatrixByColumns

public ExpressionMatrix getShuffeledMatrixByColumns(java.util.Random rand)