trans.main
Class ScanChip

java.lang.Object
  trans.main.ScanChip

public class ScanChip

extends java.lang.Object

Scores windows of intensity values using several tests.

Constructor Summary

ScanChip(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.
void	convertRatiosToPValues()
static float[][]	fetchFloatArrays(java.lang.String dir, boolean randomize) Given a directory (or a file), fetches serialized float[] from all files with the .celp extension.
static java.lang.String[]	getSCORE_DESCRIPTION()
void	importScores(Window[] windows, java.io.File importFile) Reads in a file of scores from a qvalue output file Also writes and zips an .sgr file for the qValues.
static void	main(java.lang.String[] args)
void	makeChromosomeWideScores() Makes chromosome wide scores.
void	makeSgrFile(Window[] windows, java.io.File sgrFile, int scoreIndex) Makes a xxx.sgr.zip file from a sorted Window[].
static void	printDocs()
void	printOligoRatios() Prints log2 oligo ratios.
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

ScanChip

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

Method Detail

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.

calculateRandomLabelPermutationConfidenceScores

public void calculateRandomLabelPermutationConfidenceScores()

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

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.

convertRatiosToPValues

public void convertRatiosToPValues()

printOligoRatios

public void printOligoRatios()

Prints log2 oligo ratios.

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 writes and zips an .sgr file for the qValues. Saves score in last position of the window.scores[].

fetchFloatArrays

public static float[][] fetchFloatArrays(java.lang.String dir,
                                         boolean randomize)

Given a directory (or a file), fetches serialized float[] from all files with the .celp extension. Will randomize the float[]s if so indicated.

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()

makeSgrFile

public void makeSgrFile(Window[] windows,
                        java.io.File sgrFile,
                        int scoreIndex)

Makes a xxx.sgr.zip file from a sorted Window[].