umcg.genetica.io.trityper

Class TriTyperGeneticalGenomicsDataset

java.lang.Object

umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDataset

All Implemented Interfaces:

Comparable<TriTyperGeneticalGenomicsDataset>

public final class TriTyperGeneticalGenomicsDataset
extends Object
implements Comparable<TriTyperGeneticalGenomicsDataset>

Author:

harmjan

Constructor Summary

Constructors

Constructor and Description
TriTyperGeneticalGenomicsDataset(TriTyperGeneticalGenomicsDatasetSettings settings)
TriTyperGeneticalGenomicsDataset(TriTyperGeneticalGenomicsDatasetSettings settings, Pair<List<String>,List<List<String>>> pathwayDefinitions)

Method Summary

Modifier and Type	Method and Description
int	compareTo(TriTyperGeneticalGenomicsDataset o)
boolean	equals(TriTyperGeneticalGenomicsDataset o)
DoubleMatrixDataset<String,String>	getCovariateData()
TriTyperExpressionData	getExpressionData()
int[]	getExpressionToGenotypeIdArray()
short[]	getExpressionToGenotypeIdArrayShort()
HashMap<Integer,Integer>	getExpressionToGenotypeIdHash()
TriTyperGenotypeData	getGenotypeData()
gnu.trove.map.hash.THashMap<String,String>	getGenotypeToExpressionCouplings()
HashMap<Integer,Integer>	getGenotypeToExpressionIdHash()
TriTyperGeneticalGenomicsDatasetSettings	getSettings()
int	getTotalGGSamples()
boolean	isExpressionDataLoadedCorrectly()
void	permuteCovariates(Random r)
void	permuteSampleLables(Random r) Permutes the mapping between genotype and gene expression samples
void	pruneGenotypeToExpressionCouplings()
void	resetGenotypeToExpressionCouplings()
void	setExpressionData(TriTyperExpressionData expressionData)
void	setExpressionDataLoadedCorrectly(boolean expressionDataLoadedCorrectly)
void	setGenotypeData(TriTyperGenotypeData genotypeData)
void	setGenotypeToExpressionCouplings(gnu.trove.map.hash.THashMap<String,String> genotypeToExpressionCouplings)
void	setSettings(TriTyperGeneticalGenomicsDatasetSettings settings)

Methods inherited from class java.lang.Object

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

Constructor Detail

TriTyperGeneticalGenomicsDataset

public TriTyperGeneticalGenomicsDataset(TriTyperGeneticalGenomicsDatasetSettings settings,
                                        Pair<List<String>,List<List<String>>> pathwayDefinitions)
                                 throws IOException,
                                        Exception

Throws:

IOException

Exception

TriTyperGeneticalGenomicsDataset

public TriTyperGeneticalGenomicsDataset(TriTyperGeneticalGenomicsDatasetSettings settings)
                                 throws IOException,
                                        Exception

Throws:

IOException

Exception

Method Detail

getGenotypeData

public TriTyperGenotypeData getGenotypeData()

Returns:

the genotypeData

setGenotypeData

public void setGenotypeData(TriTyperGenotypeData genotypeData)

Parameters:

genotypeData - the genotypeData to set

getExpressionData

public TriTyperExpressionData getExpressionData()

Returns:

the expressionData

setExpressionData

public void setExpressionData(TriTyperExpressionData expressionData)

Parameters:

expressionData - the expressionData to set

getGenotypeToExpressionCouplings

public gnu.trove.map.hash.THashMap<String,String> getGenotypeToExpressionCouplings()

Returns:

the genotypeToExpressionCouplings

setGenotypeToExpressionCouplings

public void setGenotypeToExpressionCouplings(gnu.trove.map.hash.THashMap<String,String> genotypeToExpressionCouplings)

Parameters:

genotypeToExpressionCouplings - the genotypeToExpressionCouplings to set

getSettings

public TriTyperGeneticalGenomicsDatasetSettings getSettings()

Returns:

the settings

setSettings

public void setSettings(TriTyperGeneticalGenomicsDatasetSettings settings)

Parameters:

settings - the settings to set

getTotalGGSamples

public int getTotalGGSamples()

getExpressionToGenotypeIdArray

public int[] getExpressionToGenotypeIdArray()

getExpressionToGenotypeIdArrayShort

public short[] getExpressionToGenotypeIdArrayShort()

compareTo

public int compareTo(TriTyperGeneticalGenomicsDataset o)

Specified by:

compareTo in interface Comparable<TriTyperGeneticalGenomicsDataset>

equals

public boolean equals(TriTyperGeneticalGenomicsDataset o)

permuteSampleLables

public void permuteSampleLables(Random r)

Permutes the mapping between genotype and gene expression samples

permuteCovariates

public void permuteCovariates(Random r)

resetGenotypeToExpressionCouplings

public void resetGenotypeToExpressionCouplings()
                                        throws IOException

Throws:

IOException

pruneGenotypeToExpressionCouplings

public void pruneGenotypeToExpressionCouplings()

getGenotypeToExpressionIdHash

public HashMap<Integer,Integer> getGenotypeToExpressionIdHash()

getExpressionToGenotypeIdHash

public HashMap<Integer,Integer> getExpressionToGenotypeIdHash()

isExpressionDataLoadedCorrectly

public boolean isExpressionDataLoadedCorrectly()

Returns:

the expressionDataLoadedCorrectly

setExpressionDataLoadedCorrectly

public void setExpressionDataLoadedCorrectly(boolean expressionDataLoadedCorrectly)

Parameters:

expressionDataLoadedCorrectly - the expressionDataLoadedCorrectly to set

getCovariateData

public DoubleMatrixDataset<String,String> getCovariateData()