umcg.genetica.io.trityper

Class TriTyperExpressionData

java.lang.Object

umcg.genetica.io.trityper.TriTyperExpressionData

public class TriTyperExpressionData
extends Object

Author:

harmjan // rows: individuals cols: probes

Constructor Summary

Constructors

Constructor and Description
TriTyperExpressionData()
TriTyperExpressionData(String loc, String probeAnnotationLoc, String platform, boolean cistrans)

Method Summary

Modifier and Type	Method and Description
void	calcAndSubtractMean()
void	calcMeanAndVariance()
void	confineToProbes(gnu.trove.set.hash.THashSet<String> probes)
String[]	getAnnotation()
byte[]	getChr()
int[]	getChrStart()
int[]	getChrStop()
String[]	getColNames()
gnu.trove.map.hash.TObjectIntHashMap<String>	getColNameToId()
Integer	getIndividualId(String key)
String[]	getIndividuals()
gnu.trove.map.hash.TObjectIntHashMap<String>	getIndividualToId()
double[][]	getMatrix()
double[]	getOriginalProbeMean()
double[]	getOriginalProbeVariance()
double[]	getProbeMean()
String[]	getProbes()
gnu.trove.map.hash.TObjectIntHashMap<String>	getProbeToId()
double[]	getProbeVariance()
String[]	getRowNames()
gnu.trove.map.hash.TObjectIntHashMap<String>	getRowNameToId()
boolean	load(String loc, String probeAnnotationLoc, String platform, boolean cistrans)
void	pruneAndReorderSamples(List<String> colObjects)
void	rankAllExpressionData(boolean rankWithTies) Ranks all the expressiondata available in rawData
void	setAnnotation(String[] annotation)
void	setChr(byte[] chr)
void	setChrStart(int[] chrStart)
void	setChrStop(int[] chrStop)
void	setColNames(String[] colNames)
void	setColNameToId(gnu.trove.map.hash.TObjectIntHashMap<String> colNameToId)
void	setConfineToProbesThatMapToAnyChromosome(boolean chr)
void	setConfineToProbesThatMapToChromosome(Integer chr)
void	setIncludeIndividuals(gnu.trove.set.hash.THashSet<String> includedIndividuals)
void	setMatrix(double[][] matrix)
void	setPathwayDefinitions(Pair<List<String>,List<List<String>>> pathwayDefinitions)
void	setRowNames(String[] rowNames)
void	setRowNameToId(gnu.trove.map.hash.TObjectIntHashMap<String> rowNameToId)

Methods inherited from class java.lang.Object

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

Constructor Detail

TriTyperExpressionData

public TriTyperExpressionData()

TriTyperExpressionData

public TriTyperExpressionData(String loc,
                              String probeAnnotationLoc,
                              String platform,
                              boolean cistrans)
                       throws IOException

Throws:

IOException

Method Detail

getRowNames

public String[] getRowNames()

Returns:

the rowNames

setRowNames

public void setRowNames(String[] rowNames)

Parameters:

rowNames - the rowNames to set

getRowNameToId

public gnu.trove.map.hash.TObjectIntHashMap<String> getRowNameToId()

Returns:

the rowNameToId

setRowNameToId

public void setRowNameToId(gnu.trove.map.hash.TObjectIntHashMap<String> rowNameToId)

Parameters:

rowNameToId - the rowNameToId to set

getColNames

public String[] getColNames()

Returns:

the colNames

setColNames

public void setColNames(String[] colNames)

Parameters:

colNames - the colNames to set

getColNameToId

public gnu.trove.map.hash.TObjectIntHashMap<String> getColNameToId()

Returns:

the colNameToId

setColNameToId

public void setColNameToId(gnu.trove.map.hash.TObjectIntHashMap<String> colNameToId)

Parameters:

colNameToId - the colNameToId to set

getMatrix

public double[][] getMatrix()

Returns:

the matrix

setMatrix

public void setMatrix(double[][] matrix)

Parameters:

matrix - the matrix to set

setIncludeIndividuals

public void setIncludeIndividuals(gnu.trove.set.hash.THashSet<String> includedIndividuals)

setConfineToProbesThatMapToAnyChromosome

public void setConfineToProbesThatMapToAnyChromosome(boolean chr)

setConfineToProbesThatMapToChromosome

public void setConfineToProbesThatMapToChromosome(Integer chr)

confineToProbes

public void confineToProbes(gnu.trove.set.hash.THashSet<String> probes)

load

public final boolean load(String loc,
                          String probeAnnotationLoc,
                          String platform,
                          boolean cistrans)
                   throws IOException

Throws:

IOException

getChrStart

public int[] getChrStart()

Returns:

the chrStart

setChrStart

public void setChrStart(int[] chrStart)

Parameters:

chrStart - the chrStart to set

getChrStop

public int[] getChrStop()

Returns:

the chrStop

setChrStop

public void setChrStop(int[] chrStop)

Parameters:

chrStop - the chrStop to set

getAnnotation

public String[] getAnnotation()

Returns:

the annotation

setAnnotation

public void setAnnotation(String[] annotation)

Parameters:

annotation - the annotation to set

getChr

public byte[] getChr()

Returns:

the chr

setChr

public void setChr(byte[] chr)

Parameters:

chr - the chr to set

getIndividuals

public String[] getIndividuals()

getProbes

public String[] getProbes()

getIndividualToId

public gnu.trove.map.hash.TObjectIntHashMap<String> getIndividualToId()

getProbeToId

public gnu.trove.map.hash.TObjectIntHashMap<String> getProbeToId()

getIndividualId

public Integer getIndividualId(String key)

calcMeanAndVariance

public void calcMeanAndVariance()

calcAndSubtractMean

public void calcAndSubtractMean()

getProbeVariance

public double[] getProbeVariance()

getProbeMean

public double[] getProbeMean()

getOriginalProbeVariance

public double[] getOriginalProbeVariance()

getOriginalProbeMean

public double[] getOriginalProbeMean()

rankAllExpressionData

public void rankAllExpressionData(boolean rankWithTies)

Ranks all the expressiondata available in rawData

pruneAndReorderSamples

public void pruneAndReorderSamples(List<String> colObjects)

setPathwayDefinitions

public void setPathwayDefinitions(Pair<List<String>,List<List<String>>> pathwayDefinitions)