umcg.genetica.methylation

Class AssociatingPcasWithAnnotation

java.lang.Object

umcg.genetica.methylation.AssociatingPcasWithAnnotation

public class AssociatingPcasWithAnnotation
extends Object

Author:

MarcJan & Juha

Constructor Summary

Constructors

Constructor and Description
AssociatingPcasWithAnnotation()

Method Summary

Modifier and Type	Method and Description
static void	associateAnovaScoreAndItemOfInterest(DoubleMatrixDataset<String,String> doubleMatrix, HashMap<String,HashMap<String,String>> interestSets) Test for difference between all GSE groups with Anova.
static void	associateScoreAndItemOfInterest(DoubleMatrixDataset<String,String> doubleMatrix, HashMap<String,HashMap<String,String>> interestSets, ArrayList<String> entries) Test for difference between 2 groups with T-test.
static void	correlateScoreAndItemOfInterest(DoubleMatrixDataset<String,String> doubleMatrix, HashMap<String,HashMap<String,String>> interestSets, String outfile, boolean samplesOnRows) Correlate values of interest to age
static void	main(String[] args)
static String[]	readGeneNamesForProbes(String filename, List<String> probes)

Methods inherited from class java.lang.Object

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

Constructor Detail

AssociatingPcasWithAnnotation

public AssociatingPcasWithAnnotation()

Method Detail

main

public static void main(String[] args)
                 throws IOException,
                        ClassNotFoundException

Parameters:

args - the command line arguments

Throws:

IOException

ClassNotFoundException

associateScoreAndItemOfInterest

public static void associateScoreAndItemOfInterest(DoubleMatrixDataset<String,String> doubleMatrix,
                                                   HashMap<String,HashMap<String,String>> interestSets,
                                                   ArrayList<String> entries)

Test for difference between 2 groups with T-test.

Parameters:

doubleMatrix -

interestSets -

entries - names of the two groups

readGeneNamesForProbes

public static String[] readGeneNamesForProbes(String filename,
                                              List<String> probes)
                                       throws IOException

Throws:

IOException

correlateScoreAndItemOfInterest

public static void correlateScoreAndItemOfInterest(DoubleMatrixDataset<String,String> doubleMatrix,
                                                   HashMap<String,HashMap<String,String>> interestSets,
                                                   String outfile,
                                                   boolean samplesOnRows)
                                            throws IOException

Correlate values of interest to age

Parameters:

doubleMatrix -

interestSets -

Throws:

IOException

associateAnovaScoreAndItemOfInterest

public static void associateAnovaScoreAndItemOfInterest(DoubleMatrixDataset<String,String> doubleMatrix,
                                                        HashMap<String,HashMap<String,String>> interestSets)

Test for difference between all GSE groups with Anova.

Parameters:

doubleMatrix -

interestSets -

entries - names of the two groups