nl.umcg.bondermj.pcoa

Class DoPcoa

java.lang.Object

nl.umcg.bondermj.pcoa.DoPcoa

public class DoPcoa
extends Object

Author:

MarcJan

Field Summary

Fields

Modifier and Type	Field and Description
static NumberFormat	DEFAULT_NUMBER_FORMATTER

Constructor Summary

Constructors

Constructor and Description
DoPcoa()

Method Summary

Modifier and Type	Method and Description
static void	calculateColtPCA(DoubleMatrixDataset<String,String> dataset, cern.colt.matrix.tdouble.DoubleMatrix2D CorMatrix, String fileNamePrefix, Integer nrOfPCsToCalculate) Calculate Colt PCA scores Matrix contains the correlation, covariation, bray curtis distance or city block distance.
static void	calculateMtjPCA(DoubleMatrixDataset<String,String> dataset, cern.colt.matrix.tdouble.DoubleMatrix2D CorMatrix, String fileNamePrefix, Integer nrOfPCsToCalculate) Calculate MTJ PCA scores Matrix contains the correlation, covariation, bray curtis distance or city block distance.
static void	generatePcCorrectedData(String fileNamePrefix, String PcaFile, String eigenVectorFile, int startSize, int nrPCAsOverSamplesToRemove, int nrIntermediatePCAsOverSamplesToRemoveToOutput)
static void	generatePcCorrectedDataWithSkipping(String fileNamePrefix, String PcaFile, String eigenVectorFile, int startSize, int nrPCAsOverSamplesToRemove, int nrIntermediatePCAsOverSamplesToRemoveToOutput, ArrayList<String> compSkipList)
static boolean	isInteger(String string)
static void	main(String... args)
static void	regressOutPCs(DoubleMatrixDataset<String,String> dataset, String fileNamePrefix, String PcaFile, String eigenVectorFile, int nrPCAsOverSamplesToRemove, int nrIntermediatePCAsOverSamplesToRemoveToOutput)

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_NUMBER_FORMATTER

public static final NumberFormat DEFAULT_NUMBER_FORMATTER

Constructor Detail

DoPcoa

public DoPcoa()

Method Detail

main

public static void main(String... args)
                 throws IOException,
                        Exception

Parameters:

args - the command line arguments

Throws:

IOException

Exception

calculateColtPCA

public static void calculateColtPCA(DoubleMatrixDataset<String,String> dataset,
                                    cern.colt.matrix.tdouble.DoubleMatrix2D CorMatrix,
                                    String fileNamePrefix,
                                    Integer nrOfPCsToCalculate)
                             throws IOException

Calculate Colt PCA scores Matrix contains the correlation, covariation, bray curtis distance or city block distance.

Parameters:

dataset -

CorMatrix -

fileNamePrefix -

nrOfPCsToCalculate -

Throws:

IOException

calculateMtjPCA

public static void calculateMtjPCA(DoubleMatrixDataset<String,String> dataset,
                                   cern.colt.matrix.tdouble.DoubleMatrix2D CorMatrix,
                                   String fileNamePrefix,
                                   Integer nrOfPCsToCalculate)
                            throws IOException

Calculate MTJ PCA scores Matrix contains the correlation, covariation, bray curtis distance or city block distance.

Parameters:

dataset -

CorMatrix -

fileNamePrefix -

nrOfPCsToCalculate -

Throws:

IOException

regressOutPCs

public static void regressOutPCs(DoubleMatrixDataset<String,String> dataset,
                                 String fileNamePrefix,
                                 String PcaFile,
                                 String eigenVectorFile,
                                 int nrPCAsOverSamplesToRemove,
                                 int nrIntermediatePCAsOverSamplesToRemoveToOutput)
                          throws IOException

Throws:

IOException

generatePcCorrectedDataWithSkipping

public static void generatePcCorrectedDataWithSkipping(String fileNamePrefix,
                                                       String PcaFile,
                                                       String eigenVectorFile,
                                                       int startSize,
                                                       int nrPCAsOverSamplesToRemove,
                                                       int nrIntermediatePCAsOverSamplesToRemoveToOutput,
                                                       ArrayList<String> compSkipList)
                                                throws IOException

Throws:

IOException

generatePcCorrectedData

public static void generatePcCorrectedData(String fileNamePrefix,
                                           String PcaFile,
                                           String eigenVectorFile,
                                           int startSize,
                                           int nrPCAsOverSamplesToRemove,
                                           int nrIntermediatePCAsOverSamplesToRemoveToOutput)
                                    throws IOException

Throws:

IOException

isInteger

public static boolean isInteger(String string)