public class TriTyperExpressionData extends Object
| Constructor and Description |
|---|
TriTyperExpressionData() |
TriTyperExpressionData(String loc,
String probeAnnotationLoc,
String platform,
boolean cistrans) |
| 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) |
public TriTyperExpressionData()
public TriTyperExpressionData(String loc, String probeAnnotationLoc, String platform, boolean cistrans) throws IOException
IOExceptionpublic String[] getRowNames()
public void setRowNames(String[] rowNames)
rowNames - the rowNames to setpublic gnu.trove.map.hash.TObjectIntHashMap<String> getRowNameToId()
public void setRowNameToId(gnu.trove.map.hash.TObjectIntHashMap<String> rowNameToId)
rowNameToId - the rowNameToId to setpublic String[] getColNames()
public void setColNames(String[] colNames)
colNames - the colNames to setpublic gnu.trove.map.hash.TObjectIntHashMap<String> getColNameToId()
public void setColNameToId(gnu.trove.map.hash.TObjectIntHashMap<String> colNameToId)
colNameToId - the colNameToId to setpublic double[][] getMatrix()
public void setMatrix(double[][] matrix)
matrix - the matrix to setpublic void setIncludeIndividuals(gnu.trove.set.hash.THashSet<String> includedIndividuals)
public void setConfineToProbesThatMapToAnyChromosome(boolean chr)
public void setConfineToProbesThatMapToChromosome(Integer chr)
public void confineToProbes(gnu.trove.set.hash.THashSet<String> probes)
public final boolean load(String loc, String probeAnnotationLoc, String platform, boolean cistrans) throws IOException
IOExceptionpublic int[] getChrStart()
public void setChrStart(int[] chrStart)
chrStart - the chrStart to setpublic int[] getChrStop()
public void setChrStop(int[] chrStop)
chrStop - the chrStop to setpublic String[] getAnnotation()
public void setAnnotation(String[] annotation)
annotation - the annotation to setpublic byte[] getChr()
public void setChr(byte[] chr)
chr - the chr to setpublic String[] getIndividuals()
public String[] getProbes()
public gnu.trove.map.hash.TObjectIntHashMap<String> getIndividualToId()
public gnu.trove.map.hash.TObjectIntHashMap<String> getProbeToId()
public void calcMeanAndVariance()
public void calcAndSubtractMean()
public double[] getProbeVariance()
public double[] getProbeMean()
public double[] getOriginalProbeVariance()
public double[] getOriginalProbeMean()
public void rankAllExpressionData(boolean rankWithTies)
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