expr
Class CorrelationMaps

java.lang.Object
  expr.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()