trans.cel
Class QuantileNormalization

java.lang.Object
  trans.cel.QuantileNormalization

public class QuantileNormalization

extends java.lang.Object

Performs quantile normalization on arrays of double values. Arrays must be of equal length. Note: median scaling can introduce an annoying periodicity into the intensity measurements that is apparent in histograms. This is not a bug. An implementation of: Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 2003 Jan 22;19(2):185-93.

Constructor Summary

QuantileNormalization()

Method Summary

void	calculateChromControlSpecificMedian(java.lang.String[] chrNameControls) Given chromosome names (e.g.
double	calculateMedianOfChromosome(Quantile[] intensities, java.lang.String chromosomeName) Looks in the tpmapInfo for the appropriate chromosome, extracts the intensities from the Quantile[], calculates a median.
float[][]	extractNormalizedValues() Extracts out the normalized values regenerating the original float[][] except the scores have been quantile normalized.
float[]	fetchControlIntensities(Quantile[] q) Uses the control indexes to fetch the control intensities from the Quantile[].
static double	fetchMedianQuantileValue(Quantile[] m) Calculates the median intensity of a sorted Quantile[].
java.io.File[]	getCelpFiles()
ControlStats[]	getControlStats()
float[][]	getIntensities()
Quantile[][]	getQuantiles() Fetches an array of sorted normalized Quantiles
int	getTargetMedian()
boolean	isUseMMData()
void	loadIntensityArrays(java.io.File[] celaMapFiles) Fetch intensity arrays from .celaMap files.
void	makeControlStats() Instantiates a ControlStats object for each Quantile[] object.
static Quantile[][]	makeQuantiles(float[][] values) Makes a Quantile[][] given float[][] where the quantile.position is assigned its array index position and the quantile.value is assigned the float value.
void	medianScaleIntensities() Median scale current intensity values.
static void	normalizeQuantileArrayScores(Quantile[][] quantiles) Takes arrays of Quantile, and averages the values for a given array index.
static float	percentile(Quantile[] sortedQs, double percentile) Returns the value of a given percentile from a SORTED Quantile array.
void	prependTargetMedianInControlStats()
void	printIntensityStats() Prints statistics about the current intensity float[][] arrays
void	quantileNormalize() Performs a median scaling then quantile normalization of the loaded float[replicas][intensities].
void	saveAndNullQuantiles() Takes the Quantile[][], fetches the float[] values for each, nulls the Quantile[], saves the float[] to disk.
void	saveIntensities() Saves intensities, one float[] for each replica.
void	scaleQuantileArraysByControlIntensities() Scales a quantile array that is sorted by original position in the MapFeature[] using the median value of the control intensities.
static void	scaleQuantileArraysByMedian(Quantile[][] quantiles, double targetMedian) Takes arrays of Quantile that have been sorted by value, and scales their values to the target median.
void	setControlChromosomeNames(java.lang.String[] controlChromosomeNames)
void	setControlIndexes(int[][] controlIndexes)
void	setIntensities(float[][] intensities)
void	setModelValuesForScaling(double[] modelValuesForScaling)
void	setQuantiles(Quantile[][] quantiles)
void	setScaleByControlStats(boolean scaleByControlStats)
void	setTargetMedian(int targetMedian)
void	setTpmapInfo(java.util.ArrayList tpmapInfo)
void	setUseMMData(boolean useMMData)
void	sortQuantileArrays(Quantile[][] q) Sorts quantile arrays based on comparator, either position or intensity value.
void	splineNormalize() Uses a cubic spline and user defined regions to non-linearly scale the data.
static float[]	transformPMMM(float[] f) Performs a max(PM-MM,1) on the float array where MM is just after each PM.

Methods inherited from class java.lang.Object

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

Constructor Detail

QuantileNormalization

public QuantileNormalization()

Method Detail

quantileNormalize

public void quantileNormalize()

Performs a median scaling then quantile normalization of the loaded float[replicas][intensities].

splineNormalize

public void splineNormalize()

Uses a cubic spline and user defined regions to non-linearly scale the data.

prependTargetMedianInControlStats

public void prependTargetMedianInControlStats()

calculateChromControlSpecificMedian

public void calculateChromControlSpecificMedian(java.lang.String[] chrNameControls)

Given chromosome names (e.g. chrGapdh, chrActb) will calculate the median intensities. Sets the values and names in the ControlStats[]. Don't forget to call makeControlStats().

makeControlStats

public void makeControlStats()

Instantiates a ControlStats object for each Quantile[] object.

calculateMedianOfChromosome

public double calculateMedianOfChromosome(Quantile[] intensities,
                                          java.lang.String chromosomeName)

Looks in the tpmapInfo for the appropriate chromosome, extracts the intensities from the Quantile[], calculates a median. Returns -1 if no chromosome found.

medianScaleIntensities

public void medianScaleIntensities()

Median scale current intensity values.

printIntensityStats

public void printIntensityStats()

Prints statistics about the current intensity float[][] arrays

loadIntensityArrays

public void loadIntensityArrays(java.io.File[] celaMapFiles)

Fetch intensity arrays from .celaMap files.

saveIntensities

public void saveIntensities()

Saves intensities, one float[] for each replica.

transformPMMM

public static float[] transformPMMM(float[] f)

Performs a max(PM-MM,1) on the float array where MM is just after each PM.

saveAndNullQuantiles

public void saveAndNullQuantiles()

Takes the Quantile[][], fetches the float[] values for each, nulls the Quantile[], saves the float[] to disk. Transforms the data if mm is present.

makeQuantiles

public static Quantile[][] makeQuantiles(float[][] values)

Makes a Quantile[][] given float[][] where the quantile.position is assigned its array index position and the quantile.value is assigned the float value.

normalizeQuantileArrayScores

public static void normalizeQuantileArrayScores(Quantile[][] quantiles)

Takes arrays of Quantile, and averages the values for a given array index.

scaleQuantileArraysByMedian

public static void scaleQuantileArraysByMedian(Quantile[][] quantiles,
                                               double targetMedian)

Takes arrays of Quantile that have been sorted by value, and scales their values to the target median. This can introduce an annoying periodicity into the data.

scaleQuantileArraysByControlIntensities

public void scaleQuantileArraysByControlIntensities()

Scales a quantile array that is sorted by original position in the MapFeature[] using the median value of the control intensities. Be sure the qn array is sorted by position!

fetchControlIntensities

public float[] fetchControlIntensities(Quantile[] q)

Uses the control indexes to fetch the control intensities from the Quantile[]. Assumes the Quantile[] is sorted by position, not value! Takes the median of duplicates.

fetchMedianQuantileValue

public static double fetchMedianQuantileValue(Quantile[] m)

Calculates the median intensity of a sorted Quantile[].

percentile

public static float percentile(Quantile[] sortedQs,
                               double percentile)

Returns the value of a given percentile from a SORTED Quantile array. Percentile is from 0-1, ie 0.95 and is according to Lentner, 1982.

sortQuantileArrays

public void sortQuantileArrays(Quantile[][] q)

Sorts quantile arrays based on comparator, either position or intensity value.

extractNormalizedValues

public float[][] extractNormalizedValues()

Extracts out the normalized values regenerating the original float[][] except the scores have been quantile normalized.

getQuantiles

public Quantile[][] getQuantiles()

Fetches an array of sorted normalized Quantiles

getIntensities

public float[][] getIntensities()

setIntensities

public void setIntensities(float[][] intensities)

getTargetMedian

public int getTargetMedian()

setTargetMedian

public void setTargetMedian(int targetMedian)

setQuantiles

public void setQuantiles(Quantile[][] quantiles)

setControlIndexes

public void setControlIndexes(int[][] controlIndexes)

isUseMMData

public boolean isUseMMData()

setUseMMData

public void setUseMMData(boolean useMMData)

getControlStats

public ControlStats[] getControlStats()

setTpmapInfo

public void setTpmapInfo(java.util.ArrayList tpmapInfo)

setScaleByControlStats

public void setScaleByControlStats(boolean scaleByControlStats)

setControlChromosomeNames

public void setControlChromosomeNames(java.lang.String[] controlChromosomeNames)

setModelValuesForScaling

public void setModelValuesForScaling(double[] modelValuesForScaling)

getCelpFiles

public java.io.File[] getCelpFiles()