expr
Class CorrelationMaps

java.lang.Object
  extended byexpr.CorrelationMaps

public class CorrelationMaps
extends java.lang.Object


Field Summary
static float[] SQUARE_ROOTS
           
 
Constructor Summary
CorrelationMaps(java.lang.String[] args)
           
 
Method Summary
 void assignPValues()
          Assigns right tail -10Log10(pvalues) for each score > 0 in the CorrelationWindows
 void correlate()
          Creates CorrelationWindows and performs random trials.
static void main(java.lang.String[] args)
           
 ExpressedGene[] makeRankedFloatArrays(ExpressedGene[] ex)
          Makes and places RankedFloatArrays in each ExpressedGene, also nulls the ExpressedGene.values.
 float pairwiseCorrelationScore(ExpressedGene[] ex)
          Average coorelation coefficient * square root of number of genes.
static ExpressedGene[] parseGeneFile(java.io.File geneFile)
          Converts a tab delimited file of (name chr start stop val1 val2 ...) into an ExpressedGene[]
 void printBarFiles()
           
 void printCorrelationWindows()
          Prints a spread sheet summary and a xxx.bed file for all of the windows.
static void printDocs()
           
 void processArgs(java.lang.String[] args)
          This method will process each argument and assign new varibles
 void randomize(int index)
           
 ExpressedGene[][] window(ExpressedGene[] ex)
          Splits a chromosome of ExpressedGenes into windows based on the windowSize and minNumberGenes
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

SQUARE_ROOTS

public static final float[] SQUARE_ROOTS
Constructor Detail

CorrelationMaps

public CorrelationMaps(java.lang.String[] args)
Method Detail

printBarFiles

public void printBarFiles()

printCorrelationWindows

public void printCorrelationWindows()
Prints a spread sheet summary and a xxx.bed file for all of the windows.


assignPValues

public void assignPValues()
Assigns right tail -10Log10(pvalues) for each score > 0 in the CorrelationWindows


correlate

public void correlate()
Creates CorrelationWindows and performs random trials. Nulls various unused objects.


randomize

public void randomize(int index)

pairwiseCorrelationScore

public float pairwiseCorrelationScore(ExpressedGene[] ex)
Average coorelation coefficient * square root of number of genes.


window

public ExpressedGene[][] window(ExpressedGene[] ex)
Splits a chromosome of ExpressedGenes into windows based on the windowSize and minNumberGenes


makeRankedFloatArrays

public ExpressedGene[] makeRankedFloatArrays(ExpressedGene[] ex)
Makes and places RankedFloatArrays in each ExpressedGene, also nulls the ExpressedGene.values.


parseGeneFile

public static ExpressedGene[] parseGeneFile(java.io.File geneFile)
Converts a tab delimited file of (name chr start stop val1 val2 ...) into an ExpressedGene[]


main

public static void main(java.lang.String[] args)

processArgs

public void processArgs(java.lang.String[] args)
This method will process each argument and assign new varibles


printDocs

public static void printDocs()