trans.main
Class ScanChromosomes

java.lang.Object
  trans.main.ScanChromosomes

public class ScanChromosomes

extends java.lang.Object

Scores windows of intensity values using several tests.

Constructor Summary

ScanChromosomes(java.lang.String[] args)

Method Summary

void	addPermutatedScoresToHistogram(java.util.ArrayList windowsAL) Uses random permutation of the cel file labels to estimate a null distribution, store random scores in a histogram for p-value and FDR estimations.
void	buildExtensionSetThreshold()
void	calculateRandomLabelPermutationConfidenceScores() Takes the histogram of random permutation scores and calculates an uncorrected p-value and FDR for each real score.
static boolean	checkSizes(float[][] replicasValues) Checks to see if the number of values are the same given float[replica#][values].
void	convertRatiosToPValues()
static float[][]	fetchIntensities(java.io.File[] directories, java.lang.String fileName) Fetches a float[] from each of the directories given a fileName.
float[][]	getControlIntensities()
int	getNumPermutations()
int[]	getPositions()
java.io.File	getResultsDirectory()
static java.lang.String[]	getSCORE_DESCRIPTION()
float[][]	getTreatmentIntensities()
Window[]	getWindows()
void	importScores(Window[] windows, java.io.File importFile) Reads in a file of scores from a qvalue output file Also makes gr files for the qValues.
static void	main(java.lang.String[] args)
void	makeBarFiles(Window[] windows, java.io.File directory, int scoreIndex) Makes xxx.bar.zip files from a Window[], one per chromosome.
void	makeChromosomeWideScores() Makes chromosome wide scores.
void	makeDirectories() Makes directories and files to hold point gr files and tempRatios
static void	printDocs()
void	printOligoRatios() Prints log2 oligo ratios as a chromosome specific xxx.bar file.
void	processArgs(java.lang.String[] args) This method will process each argument and assign new varibles
double	scoreWindow(int testWindowIndex) Scores a window using a pseudo median or trimmed mean on oligo relative differences.
void	shuffleIntensities() Combines and shuffles the treatment and control intensities.

Methods inherited from class java.lang.Object

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

Constructor Detail

ScanChromosomes

public ScanChromosomes(java.lang.String[] args)

Method Detail

calculateRandomLabelPermutationConfidenceScores

public void calculateRandomLabelPermutationConfidenceScores()

Takes the histogram of random permutation scores and calculates an uncorrected p-value and FDR for each real score.

addPermutatedScoresToHistogram

public void addPermutatedScoresToHistogram(java.util.ArrayList windowsAL)

Uses random permutation of the cel file labels to estimate a null distribution, store random scores in a histogram for p-value and FDR estimations.

shuffleIntensities

public void shuffleIntensities()

Combines and shuffles the treatment and control intensities.

scoreWindow

public double scoreWindow(int testWindowIndex)

Scores a window using a pseudo median or trimmed mean on oligo relative differences. If the number of relative differences exceed the maxScores then they are randomly sampled to the number of maxScores prior to running the pseudo median. Returns 0 if using pseudoMedian and window size is < 2 or if using trm meand and window size < 3.

Returns:

trimmed mean average or pseudo median layered relative difference score -2 to 2.

makeBarFiles

public void makeBarFiles(Window[] windows,
                         java.io.File directory,
                         int scoreIndex)

Makes xxx.bar.zip files from a Window[], one per chromosome.

convertRatiosToPValues

public void convertRatiosToPValues()

printOligoRatios

public void printOligoRatios()

Prints log2 oligo ratios as a chromosome specific xxx.bar file. Convert to print a bar file directly!

makeDirectories

public void makeDirectories()

Makes directories and files to hold point gr files and tempRatios

makeChromosomeWideScores

public void makeChromosomeWideScores()

Makes chromosome wide scores.

importScores

public void importScores(Window[] windows,
                         java.io.File importFile)

Reads in a file of scores from a qvalue output file Also makes gr files for the qValues. Saves score in last position of the window.scores[].

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()

getSCORE_DESCRIPTION

public static java.lang.String[] getSCORE_DESCRIPTION()

buildExtensionSetThreshold

public void buildExtensionSetThreshold()

fetchIntensities

public static float[][] fetchIntensities(java.io.File[] directories,
                                         java.lang.String fileName)

Fetches a float[] from each of the directories given a fileName. Returns null if a file cannot be read or it is not a serialized float[].

Returns:

float[replicas][intensities]

checkSizes

public static boolean checkSizes(float[][] replicasValues)

Checks to see if the number of values are the same given float[replica#][values].

getControlIntensities

public float[][] getControlIntensities()

getNumPermutations

public int getNumPermutations()

getPositions

public int[] getPositions()

getResultsDirectory

public java.io.File getResultsDirectory()

getTreatmentIntensities

public float[][] getTreatmentIntensities()

getWindows

public Window[] getWindows()