org.systemsbiology.gaggle.experiment.gui.actions
Class CorrelationFinder

java.lang.Object
  org.systemsbiology.gaggle.experiment.gui.actions.CorrelationFinder

public class CorrelationFinder
extends java.lang.Object

This class finds the correlation between gene expression vectors. Given an ExpressionData object and a vector of expression values, it computes the normalized dot product of the expression vector of every gene in the data set with the provided vector. The target vector can be constructed in three ways; given a single gene, that gene's expression vector forms the target vector; given a set of genes, the average of their normalized expression vectors is the target vector; alternatively, a user-defined vector of sufficient length can be provided as the target vector. The various build methods build and return the correlation table, which can also be accessed later via the get method. The return value is a Map where the keys are Strings, the gene names, and the values are Double objects containing the correlation values. On any error, an empty Map is returned.

Constructor Summary

CorrelationFinder()

CorrelationFinder(DataMatrix matrix)

Method Summary

java.util.Map	buildCorrelationTable(ReadOnlyMathVector targetVector)
java.util.Map	buildCorrelationTable(java.lang.String targetName) Find the correlation of all gene expression vectors with the expression vector of the supplied gene
java.util.Map	buildCorrelationTable(java.lang.String[] targets) Find the correlation of all gene expression vectors with the average of the normalized expression vectors for the supplied list of genes.
java.util.Map	getCorrelationTable() Return the most recently computed table of correlation values as a Map where the gene name is the key and a Double object is the value.
java.util.Map	oldBuildCorrelationTable(ReadOnlyMathVector targetVector) Find the correlation of all gene expression vectors with the supplied vector which should be of the same length (i.e., the number of experimental conditions).
void	setDataMatrix(DataMatrix matrix)

Methods inherited from class java.lang.Object

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

Constructor Detail

CorrelationFinder

public CorrelationFinder()

CorrelationFinder

public CorrelationFinder(DataMatrix matrix)

Method Detail

setDataMatrix

public void setDataMatrix(DataMatrix matrix)

buildCorrelationTable

public java.util.Map buildCorrelationTable(java.lang.String targetName)

Find the correlation of all gene expression vectors with the expression vector of the supplied gene

buildCorrelationTable

public java.util.Map buildCorrelationTable(java.lang.String[] targets)

Find the correlation of all gene expression vectors with the average of the normalized expression vectors for the supplied list of genes.

buildCorrelationTable

public java.util.Map buildCorrelationTable(ReadOnlyMathVector targetVector)

oldBuildCorrelationTable

public java.util.Map oldBuildCorrelationTable(ReadOnlyMathVector targetVector)

Find the correlation of all gene expression vectors with the supplied vector which should be of the same length (i.e., the number of experimental conditions).

getCorrelationTable

public java.util.Map getCorrelationTable()

Return the most recently computed table of correlation values as a Map where the gene name is the key and a Double object is the value.