Num

Method Summary
`static double`	`antiLog(double loggedValue, int base)` Converts to unlogged value.
`static float[]`	`antiLog(float[] loggedValues, int base)` Converts an array float[] to unlogged values.
`static double[]`	`appendDouble(double[] d, double newValue)` Returns a new array with the newValue appended on the end.
`static int[][]`	`arrayList2IntArrayArray(java.util.ArrayList al)` Converts an ArrayList of int[]s to int[][].
`static double[]`	`arrayListOfDoubleToArray(java.util.ArrayList dbl)` ArrayList of Double to double[]
`static float[]`	`arrayListOfFloatToArray(java.util.ArrayList flt)` ArrayList of Float to float[]
`static double[]`	`arrayListToDoubles(java.util.ArrayList doubles)` ArrayList of Double to double[]
`static int[]`	`arrayListToInts(java.util.ArrayList integers)` ArrayList of Integer to int[]
`static double`	`aveFoldDiffCombine(int[] t, int[] c)` Calculates the average fold difference between two int[]s of the same length.
`static double`	`aveFoldDiffIndividual(int[] t, int[] c)` Calculates the average fold difference between two int[]s of the same length.
`static double`	`averageFloatArray(float[] f)` Averages a float[]
`static double[]`	`averageFloatArrays(float[][] ints)` Average float[][] values to double[], averages repeats [values][numRepeats]
`static double[]`	`averageFloatArraysFlipped(float[][] ints)` Average float[][] values to double[], averages repeats [numChips][OligoValues].
`static float[]`	`averageFloatArraysFlippedToFloat(float[][] ints)` Average float[][] values to double[], averages repeats [numChips][OligoValues].
`static float[]`	`averageFloatArraysFlippedToFloats(float[][] ints)` Average float[][] values to float[], averages repeats [numChips][OligoValues].
`static double`	`averageIntArray(int[] f)` Averages a int[]
`static double[]`	`averageIntIntArray(int[][] ints)` Average int[][] values to double[], averages repeats [numRepeats][values]
`static double[]`	`averageIntIntArray2(int[][] ints)` Average int[][] values to double[], averages values [numRepeats][values]
`static double`	`calcMaxMedianAbsoluteDifference(float[][] oligosValues)` Calculates the maximum median absolute difference between arrays of float where int[oligo index number][oligo intensity measurements]
`static double`	`calcMeanMedianAbsoluteDifference(float[][] oligosValues)` Calculates the mean of the median absolute differences between arrays of float where float[oligo index number][oligo intensity measurements]
`static double[]`	`collapseDoubleArray(double[][] fs)` Assumes equal lengths of the double[]s
`static float[]`	`collapseFloatArray(float[][] fs)` Assumes equal lengths of the float[]s
`static int[]`	`collapseIntArray(int[][] ints)` Assumes equal lengths of the int[]s
`static float[]`	`collapsePartOfAnArray(float[][] fs, int startIndex, int stopIndex)` Assumes equal lengths of the float[]s
`static float[]`	`concatinate(float[][] f)` Concatinates the float[]s, variable sizes OK.
`static float[]`	`concatinate(float[] one, float[] two)` Joins two float[]s using System.arraycopy().
`static double[]`	`convertToDouble(int[] d)` Convert to double[]
`static float[]`	`convertToFloat(int[] d)` Convert to float[]
`static int[]`	`convertToInt(double[] d)` Convert to int[]
`static int[]`	`convertToInt(float[] d)` Convert to int[]
`static double[]`	`convertToMedianZScores(double[] values)` Converts an array of values to z scores using median as appose to mean.
`static double[]`	`convertToZScores(double[] values)` Converts an array of values to z scores.
`static double[]`	`convertToZScores(double[] values, double mean, double stndDev)` Converts an array of values to z scores given their mean and standard deviation.
`static double`	`correlationCoefficient(double[] x, double[] y)` Calculates Pearson correlation coefficient, r, from two double[]s
`static double`	`correlationCoefficient(float[] x, float[] y)` Calculates Pearson correlation coefficient, r, from two float[]s.
`static double`	`correlationCoefficient(int[] x, int[] y)` Calculates Pearson correlation coefficient, r, from two int[]s.
`static int`	`countObjects(java.lang.Object[][] i)` Returns the number of objects in the arrays.
`static int`	`countOutliers(float[] f, double threshold, boolean exceedsThreshold)` Counts the number of values that are > or < threshold based on boolean.
`static int`	`countValues(int[][] i)` Returns the number of elements/ values in the array.
`static double[]`	`difference(double[] t, double[] c)` Returns the difference of each pair.
`static double[]`	`difference(int[] t, int[] c)` Returns the difference of each pair.
`static java.lang.String`	`doubleArrayToString(double[] d, int numberOfDecimalPlaces, java.lang.String delimiter)` Converts an array of double to a String with a defined number of decimal places and a delimiter.
`static java.lang.String`	`doubleArrayToStringOnlyMax(double[] d, int maxNumDec, java.lang.String delimiter)` Converts an array of double to a String with a maximal number of defined decimal places and a delimiter.
`static float[][]`	`expandFloatArray(float[] f, int numRows, int numColumns)` Converts a float[] to float[][], must be certain about the number of rows and colmns!
`static long`	`factorial(int x)` Calculates N! modified from http://www.unix.org.ua/orelly/java-ent/jnut/ch01_03.htm
`static float[]`	`fetchMatrixValues(float[][] matrix, int[][] xy)` Given a square table and a list of coordinates, will return the associated values.
`static int`	`findClosestEndIndex(int[] positions, int key)` Finds the index of the key in the int[] but wont exceed the int[index]
`static int`	`findClosestIndexToValue(float[] sortedValues, float key)` Returns the index of the closest values[index] to the key.
`static int`	`findClosestIndexToValue(int[] sortedValues, int key)` Returns the index of the closest values[index] to the key.
`static int`	`findClosestStartIndex(int[] positions, int key)` Finds the index of the key in the int[] but wont preceed the int[index]
`static float`	`findHighestFloat(float[] ints)` Finds and returns the biggest float in an float[].
`static int`	`findHighestInt(int[] ints)` Finds and returns the biggest int in an int[].
`static int`	`findMaxIntIndex(int[] ints)` Returns the first index containing the maximum value.
`static double[]`	`findMinMaxDoubleValues(double[] f)` Finds min and max values of a float array.
`static float[]`	`findMinMaxFloatArrays(float[][] f)` Finds min and max values of a float array.
`static float[]`	`findMinMaxFloatValues(float[] f)` Finds min and max values of an unsorted float array.
`static int[]`	`findMinMaxIntInt(int[][] f)` Finds min and max values of a int array.
`static int[]`	`findMinMaxIntValues(int[] f)` Finds min and max values of a int array.
`static int[]`	`findStartStopIndexes(int[] positions, int startValue, int stopValue, boolean notExact)` Finds the start and stop indexes given a sorted int[] of values and two values, one after the other, close together, otherwise just use Arrays.binarySearch.
`static boolean`	`findZeros(float[] f)` Scans a float array for zeros, if found returns true, other wise returns false.
`static java.lang.String`	`formatNumber(double num, int numberOfDecimalPlaces)` Converts a double ddd.dddddddd to a user determined number of decimal places right of the .
`static java.lang.String`	`formatNumberOneFraction(double num)` Converts a double ddd.dddddddd to sss.s
`static java.lang.String`	`formatPercentOneFraction(double num)` Converts 0.345543 to 34.6%
`static double[]`	`geoMeanFloatArraysFlipped(float[][] ints)` Takes the geometric mean of float[][] values to double[], [numChips][OligoValues], returns the values in log base 2.
`static double`	`geometricMean(double[] x)` Geometric mean.
`static double[]`	`geometricMean(float[][] ints)` Takes a geometric average of float[][] values [numChips][OligoValues].
`static float[]`	`geometricMeanRatio(float[][] t, float[][] c)` Returns the log2 ratio of each pair, takes a geometric mean of replicas.
`static double[]`	`geometricMeanSkipZeros(float[][] ints)` Takes a geometric average of float[][] values to double[], averages repeats [numChips][OligoValues].
`static float`	`getAverageInts(int start, int end)` Gets the average of the integers bracketed and including the start and end.
`static float[][]`	`identifyOutliers(float[][] f, int[][] controls, float threshold, boolean exceedsThreshold)` Loads a zeroed matrix with values that are > or < threshold based on boolean.
`static java.lang.String`	`intArrayToString(int[] d, java.lang.String delimiter)` Converts an array of int to a String seperated by the delimiter.
`static void`	`invertArray(float[] x)` Inverts the float[].
`static double[]`	`layeredLogRatios(float[][] oligoTreat, float[][] oligoCont)` Given two float[replica][values] for treat and cont, for each replica makes all pairwise log2 ratios between treat and control.
`static float[][]`	`layeredLogRatiosSeperate(float[][] treatment, float[][] control)` Given two float[replica][intensities] for treat and cont, for each oligo makes and returns all pairwise log2 ratios between treat and control replicas.
`static double[]`	`layeredRatios(float[][] oligoTreat, float[][] oligoCont)` Given two float[replica][values] for treat and cont, for each replica makes all pairwise ratios between treat and control.
`static float[][]`	`layeredRatiosSeperate(float[][] treatment, float[][] control)` Given two float[replica][intensities] for treat and cont, for each oligo makes and returns all pairwise ratios between treat and control replicas.
`static double[]`	`layeredRelativeDifferences(float[][] oligoTreat, float[][] oligoCont)` Given two float[replica][values] for treat and cont, for each replica makes all pairwise relative differences between treat and control.
`static float[][]`	`layeredRelativeDifferencesSeperate(float[][] treatment, float[][] control)` Given two float[replica][intensities] for treat and cont, for each oligo makes and returns all pairwise relative differences between treat and control replicas.
`static double[]`	`loadDoubles(java.io.File f)` Loads a column of double from a file into an array.
`static float[][]`	`loadFloatArray(int x, int y, float value)` Makes a float[x][y] and fills it with the value.
`static int[]`	`loadInts(java.io.File f)` Loads a column of ints from a file into an array.
`static float[][]`	`loadMatrixValues(float[][] matrix, int[][] xy)` Given a square table and a list of coordinates, will return the associated values in a new zeroed square table.
`static double`	`log10(double number)` Returns the LOG base 10 of the number.
`static double`	`log2(double number)` Returns the LOG base 2 of the number.
`static float`	`log2(float number)` Returns the LOG base 2 of the number.
`static void`	`log2(float[] f)` Log2s every number in the array replacing the original values.
`static void`	`log2(float[][] f)` Log2s every number in the array replacing the original values.
`static float[]`	`log2Return(float[] f)` Log2s every number in the array keeping original intact.
`static float[][]`	`log2Return(float[][] f)` Log2s every number in the array returning the values, keep original intact.
`static double[]`	`log2ReturnDouble(float[] f)` Log2s every number in the array keeping original intact.
`static double[]`	`logRatios(double[] t, double[] c)` Calculates log base 2 ratios.
`static float[]`	`logRatios(float[][] t, float[][] c)` Returns the log2 ratio of each pair, averaging replicas.
`static double[]`	`logRatios(float[] t, float[] c)` Calculates log base 2 ratios.
`static void`	`maskOutliers(float[][] f, float outlierThreshold)` Runs through float[][] setting any values that exceed the outlierThreshold to zero.
`static double`	`matScore(float[] t, float[] c)` Takes unlogged MAT normalized t-values, sorts, logs and takes a variant of a number stabilized trimmed mean ratio.
`static double`	`mean(double[] t)` Averages a double array.
`static float`	`mean(float[] t)` Averages a float array.
`static float[][]`	`mean(float[][] one, float[][] two)` Averages two float[][]s, assumes a square.
`static float[]`	`mean(float[] one, float[] two)` Averages two float[]s .
`static double`	`mean(int[] t)` Averages a int array.
`static java.lang.String`	`meanDoubles(java.util.ArrayList Doubles)` Averages an ArrayList of Double objects.
`static double`	`meanIgnoreZeros(float[] f)` Calculates a mean on the non zero floats, return zero if no non zero values were found.
`static int`	`meanIntegers(java.util.ArrayList Integers)` Averages an ArrayList of Integer objects.
`static double`	`median(double[] sorted)` Calculates Median of a sorted double[].
`static double`	`median(float[] sorted)` Calculates Median of a sorted float[].
`static double`	`median(int[] sorted)` Calculates Median of a sorted int[].
`static double`	`median(short[] sorted)` Calculates Median of a sorted short[].
`static double`	`medianAbsoluteDifference(float[] x, float[] y)` Calculates the median absolute difference.
`static java.lang.String`	`medianFloatArray(float[][] replicasIntensities)`
`static double`	`medianIgnoreZeros(float[] m)` Calculates the median value of a sorted float[] ignoring leading zero values!
`static float[][]`	`medianNormalize(float[][] f, double targetMedian)` Median normalizes an unsorted float[][] array to a given target.
`static float[]`	`medianNormalize(float[] f, float targetMedian)` Median normalize unsorted array to a given number.
`static double`	`millisecToDays(long ms)` Converts milliseconds to days.
`static double`	`minus10log10(double pvalue)` Returns the -10 * LOG base 10 of the number.
`static int[]`	`modeOfHistogram(int[] ints)` Finds mode of a int[] histogram array, assumes one peak, returns the index position, value/frequency.
`static double[]`	`pairedLogRatios(float[][] treatments, float[][] controls)` Given two float[replica][values] for treat and cont, for each replica makes matched pairwise log ratios between treat and control.
`static double[]`	`pairedRatios(float[][] treatments, float[][] controls)` Given two float[replica][values] for treat and cont, for each replica makes matched pairwise ratios between treat and control.
`static double[]`	`pairedRelativeDifferences(float[][] treatments, float[][] controls)` Given two float[replica][values] for treat and cont, for each replica makes matched pairwise relative differences between treat and control.
`static float[]`	`pairwiseMeans(float[] d)` Returns all pairwise averages.
`static double[]`	`pairwiseMeansDouble(float[] d)` Returns all pairwise averages.
`static double[]`	`parseDoubles(java.lang.String[] doubles)` Parses doubles from a String[] of doubles.
`static int`	`parseInt(java.lang.String stringInt, int failNumber)` Attemps to parse an int, returns failNumber if it fails.
`static int[]`	`parseInts(java.lang.String[] ints)` Parses ints from a String[] of ints.
`static double[]`	`partialPairwiseMeans(float[] a, float[] b)` Returns all pairwise averages between a and b but not self pairwise.
`static float`	`percentile(float[] sortedFloats, double percentile)` Returns the value of a given percentile from a SORTED array.
`static float[][]`	`pooledSubArray(float[][] treatment, float[][] control, int startIndex, int stopIndex)` Builds a pooled from part of a float[replica][intensities] for treat and control.
`static double[]`	`prependDouble(double[] d, double newValue)` Returns a new array with the newValue appended on the beginning.
`static double`	`pseudoMedian(double[] d)` Returns a Hodges-Lehmann estimator, the median of all pairwise means.
`static double`	`pseudoMedian(float[] d)` Returns a Hodges-Lehmann estimator, the median of all pairwise means.
`static double[]`	`pseudoMedian(float[][] repInt)` Calculates the pseudoMedian on each replica of intensities.
`static double[]`	`quartiles(float[] sortedFloatArray)` Calculates the Q1,Q2,and Q3 (25th, 50th, and 75th percentile).
`static void`	`randomize(float[][] f)` Randomizes the intensities, not between replicas.
`static void`	`randomize(float[] f, long seed)` Randomizes the array by permutating indexes and swapping.
`static void`	`randomizeFirstArray(float[][] f, long seed)` Randomizes the first array by permutating indexes and swapping.
`static float[]`	`randomSample(float[] x, int numToSample)` Returns an array of float[numToSample] populated with randomly picked values from x.
`static double[]`	`ratio(double[] t, double[] c)` Returns the ratio of each pair.
`static float[]`	`ratio(float[][] t, float[][] c)` Returns the ratio of each pair, averages replicas.
`static double[]`	`ratio(float[] t, float[] c)` Returns the ratio of each pair.
`static double[]`	`ratio(int[] t, double[] c)` Returns the ratio of each pair.
`static double[]`	`ratio(int[] t, int[] c)` Returns the ratio of each pair.
`static double`	`relativeDifference(double t, double c)` Calculates a relative difference.
`static float[]`	`relativeDifferences(float[][] t, float[][] c)` Returns the relative difference of each pair, averages replicas.
`static double[]`	`relativeDifferences(float[] t, float[] c)` Calculates relative differences.
`static double`	`relativeDifferenceToLog2Ratio(double relDiff)` Converter
`static float[]`	`relativeDifferenceToLog2Ratio(float[] relDiff)` Converter
`static double[]`	`removeNaNInfinite(double[] d)` Removes any NaN or Infinite
`static float[]`	`removeZeroValues(float[] f)` Remove zero values from float array.
`static float[][]`	`removeZeroValues(float[][] f)` Provide a float[2][0], will remove zeros from both and there matched pair.
`static float[][][]`	`removeZeroValues(float[][] t, float[][] c)` Removes zero values and their assoicated values from all arrays.
`static float[][]`	`rotateClockwise(float[][] matrix)` Rotates a square matrix 90 degrees Clock Wise?
`static float[][]`	`rotateCounterClockwise(float[][] matrix)` Rotates a square matrix 90 degrees CounterClockWise?
`static double[]`	`round(double[] d, int numDecimals)` Rounds a double[] based on number of desired decimals, ie 1 = x.x, 2 = x.xx limited to 6
`static double`	`round(double d, int numDecimals)` Rounds a double based on number of desired decimals, ie 1 = x.x, 2 = x.xx limited to 6
`static float[]`	`sam(float[] t, float[] c, double fudge)` Calculates the SAM d statistic, similar to a t-statistic with a bit of fudge added into the denominator to control for zero variance conditions.
`static void`	`saveMatrixValues(float[][] matrix, int[][] xy, float threshold, java.io.File f)` Given a square table and a list of coordinates, save the associated values.
`static double[]`	`smoothScores(double[] scores, int[] positions, int windowSize)` Uses a sliding window to smooth the scores applying a trimmed mean (drop 1 from ends) to the scores found within the window.
`static float[]`	`squareRoots(int num)` Returns the integer square root from zero to num.
`static double`	`standardDeviation(double[] x)` Calculates standard deviation of an double[]
`static double`	`standardDeviation(double[] x, double mean)` Calculates standard deviation of a double[] and mean.
`static double`	`standardDeviation(float[] x)` Calculates standard deviation of an float[]
`static double`	`standardDeviation(float[] x, double mean)` Calculates standard deviation of an float[] given a mean.
`static double`	`standardDeviation(int[] x)` Calculates standard deviation of an int[]
`static double`	`standardDeviation(int[] x, double mean)` Calculates standard deviation of an int[] and mean.
`static double`	`standardDeviationOfDifference(int[] t, int[] c)` Calculates the standard deviation of the difference between two int[]s of the same length.
`static double`	`standardError(double[] x, double mean)` Calculates standard error of a double[] given it's mean.
`static void`	`statFloatArray(float[] f, boolean printHistogram)` Calculates Min, Max, Mean, Median, Mode, and Histogram/10 for a Float[]
`static int[]`	`stringArrayToInts(java.lang.String s, java.lang.String delimiter)` Given a String of ints delimited by something, will parse or return null.
`static float[][]`	`subArray(float[][] intensities, int startIndex, int stopIndex)` Builds a sub array from part of a float[replica][intensities].
`static int`	`sumIntArray(int[] ints)` Sums an int array
`static double`	`trimmedMean(double[] sortedFloat, double fraction)` Trims the fraction off the top and bottom, returns the mean of the remainder, rounds trimming # up.
`static double`	`trimmedMean(double[] sortedDouble, int trimNumber)` Makes a trimmed mean, note the trim number is not a % but the number of values to drop from the beginning and end of the ordered set.
`static double`	`trimmedMean(float[] sortedFloat, double fraction)` Trims the fraction off the top and bottom, returns the mean of the remainder, rounds trimming # up.
`static double`	`trimmedMean(float[] sortedFloat, int trimNumber)` Makes a trimmed mean, note the trim number is not a % but the number of values to drop from the beginning and end of the ordered set.
`static float[][]`	`trimOutliers(float[][] f, float cutoff, float replacement)` For each f[replica][]Sets values exceeding the cutoff to the default.
`static float[]`	`trimOutliers(float[] f, float cutoff, float replacement)` Sets values exceeding the cutoff to the default.
`static double`	`tukeyBiWeight(double[] x)` Calculates a one-step tukey biweight estimator using 5 as the tuning constant and adding 0.0001 to the denominator to avoid dividing by zero, Affy's params.
`static double[]`	`windowAverageScores(double[] scores, int windowSize)` Slides a window along an array, one index at a time, averaging the contents.
`static float[]`	`windowAverageScores(float[] scores, int windowSize)` Slides a window along an array, one index at a time, averaging the contents.
`static float[]`	`windowAverageScoresIgnoreScore(float[][] scores, float scoreToIgnore, int windowSize)` Slides a window along an array, one index at a time, averaging the contents, ignores zero values.
`static float[]`	`windowAverageScoresIgnoreScore(float[] scores, float scoreToIgnore, int windowSize)` Slides a window along an array, one index at a time, averaging the contents.
`static double[]`	`windowAverageScoresIgnoreZeros(double[] scores, int windowSize)` Slides a window along an array, one index at a time, averaging the contents, ignores zero values.
`static float[][]`	`zeroedFloatArray(int x, int y)` Makes a float[x][y] and fills it with zeros.

Methods inherited from class java.lang.Object

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

Field Detail

log10

public static final double log10

log2

public static final double log2

Constructor Detail

Num

public Num()

Method Detail

relativeDifferenceToLog2Ratio

public static float[] relativeDifferenceToLog2Ratio(float[] relDiff)

Converter

relativeDifferenceToLog2Ratio

public static double relativeDifferenceToLog2Ratio(double relDiff)

Converter

millisecToDays

public static double millisecToDays(long ms)

Converts milliseconds to days.

invertArray

public static void invertArray(float[] x)

Inverts the float[].

factorial

public static long factorial(int x)

Calculates N! modified from http://www.unix.org.ua/orelly/java-ent/jnut/ch01_03.htm

arrayList2IntArrayArray

public static int[][] arrayList2IntArrayArray(java.util.ArrayList al)

Converts an ArrayList of int[]s to int[][].

antiLog

public static double antiLog(double loggedValue,
                             int base)

Converts to unlogged value.

antiLog

public static float[] antiLog(float[] loggedValues,
                              int base)

Converts an array float[] to unlogged values.

findZeros

public static boolean findZeros(float[] f)

Scans a float array for zeros, if found returns true, other wise returns false.

rotateCounterClockwise

public static float[][] rotateCounterClockwise(float[][] matrix)

Rotates a square matrix 90 degrees CounterClockWise?

rotateClockwise

public static float[][] rotateClockwise(float[][] matrix)

Rotates a square matrix 90 degrees Clock Wise?

findMaxIntIndex

public static int findMaxIntIndex(int[] ints)

Returns the first index containing the maximum value.

log2

public static void log2(float[][] f)

Log2s every number in the array replacing the original values.

log2Return

public static float[][] log2Return(float[][] f)

Log2s every number in the array returning the values, keep original intact.

log2

public static void log2(float[] f)

Log2s every number in the array replacing the original values.

log2Return

public static float[] log2Return(float[] f)

Log2s every number in the array keeping original intact.

log2ReturnDouble

public static double[] log2ReturnDouble(float[] f)

Log2s every number in the array keeping original intact.

parseDoubles

public static double[] parseDoubles(java.lang.String[] doubles)

Parses doubles from a String[] of doubles. Returns null if a parsing error is encountered.

parseInts

public static int[] parseInts(java.lang.String[] ints)

Parses ints from a String[] of ints. Returns null if a parsing error is encountered.

convertToZScores

public static double[] convertToZScores(double[] values,
                                        double mean,
                                        double stndDev)

Converts an array of values to z scores given their mean and standard deviation.

convertToZScores

public static double[] convertToZScores(double[] values)

Converts an array of values to z scores.

convertToMedianZScores

public static double[] convertToMedianZScores(double[] values)

Converts an array of values to z scores using median as appose to mean.

appendDouble

public static double[] appendDouble(double[] d,
                                    double newValue)

Returns a new array with the newValue appended on the end.

prependDouble

public static double[] prependDouble(double[] d,
                                     double newValue)

Returns a new array with the newValue appended on the beginning.

tukeyBiWeight

public static double tukeyBiWeight(double[] x)

Calculates a one-step tukey biweight estimator using 5 as the tuning constant and adding 0.0001 to the denominator to avoid dividing by zero, Affy's params. If all zeros are submitted then returns zero.

geometricMean

public static double geometricMean(double[] x)

Geometric mean. Cannot have any zeros or negative numbers in the double[].

percentile

public static float percentile(float[] sortedFloats,
                               double percentile)

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

maskOutliers

public static void maskOutliers(float[][] f,
                                float outlierThreshold)

Runs through float[][] setting any values that exceed the outlierThreshold to zero. Assumes float[i]s are equal length.

countValues

public static int countValues(int[][] i)

Returns the number of elements/ values in the array.

countObjects

public static int countObjects(java.lang.Object[][] i)

Returns the number of objects in the arrays.

countOutliers

public static int countOutliers(float[] f,
                                double threshold,
                                boolean exceedsThreshold)

Counts the number of values that are > or < threshold based on boolean. Returns - number of outliers > or < threshold Param - exceedsThreshold, boolean flag when true counts the number that exceed the threshold, when false the number less than the threshold.

identifyOutliers

public static float[][] identifyOutliers(float[][] f,
                                         int[][] controls,
                                         float threshold,
                                         boolean exceedsThreshold)

Loads a zeroed matrix with values that are > or < threshold based on boolean. Returns a loaded zeroed matrix. Param exceedsThreshold, boolean flag when true returns the values that exceed the threshold, less than the threshold.

fetchMatrixValues

public static float[] fetchMatrixValues(float[][] matrix,
                                        int[][] xy)

Given a square table and a list of coordinates, will return the associated values.

saveMatrixValues

public static void saveMatrixValues(float[][] matrix,
                                    int[][] xy,
                                    float threshold,
                                    java.io.File f)

Given a square table and a list of coordinates, save the associated values.

loadMatrixValues

public static float[][] loadMatrixValues(float[][] matrix,
                                         int[][] xy)

Given a square table and a list of coordinates, will return the associated values in a new zeroed square table.

quartiles

public static double[] quartiles(float[] sortedFloatArray)

Calculates the Q1,Q2,and Q3 (25th, 50th, and 75th percentile). Ignores the middle value in calculating Q1 and Q3 if the array length is odd. Don't forget to sort the array!

zeroedFloatArray

public static float[][] zeroedFloatArray(int x,
                                         int y)

Makes a float[x][y] and fills it with zeros.

loadFloatArray

public static float[][] loadFloatArray(int x,
                                       int y,
                                       float value)

Makes a float[x][y] and fills it with the value.

randomSample

public static float[] randomSample(float[] x,
                                   int numToSample)

Returns an array of float[numToSample] populated with randomly picked values from x.

randomize

public static void randomize(float[] f,
                             long seed)

Randomizes the array by permutating indexes and swapping. Fast. Can set seedMultiplier or vary it to be sure and get diff

randomizeFirstArray

public static void randomizeFirstArray(float[][] f,
                                       long seed)

Randomizes the first array by permutating indexes and swapping. Fast. Shuffles f[shuffle][].

randomize

public static void randomize(float[][] f)

Randomizes the intensities, not between replicas.

layeredRatiosSeperate

public static float[][] layeredRatiosSeperate(float[][] treatment,
                                              float[][] control)

Given two float[replica][intensities] for treat and cont, for each oligo makes and returns all pairwise ratios between treat and control replicas.

Returns:: float[oligo index][all t/c ratios]

layeredRelativeDifferencesSeperate

public static float[][] layeredRelativeDifferencesSeperate(float[][] treatment,
                                                           float[][] control)

Given two float[replica][intensities] for treat and cont, for each oligo makes and returns all pairwise relative differences between treat and control replicas.

Returns:: float[oligo index][all relative differences]

layeredRelativeDifferences

public static double[] layeredRelativeDifferences(float[][] oligoTreat,
                                                  float[][] oligoCont)

Given two float[replica][values] for treat and cont, for each replica makes all pairwise relative differences between treat and control. Returns as a big pool.

layeredLogRatiosSeperate

public static float[][] layeredLogRatiosSeperate(float[][] treatment,
                                                 float[][] control)

Given two float[replica][intensities] for treat and cont, for each oligo makes and returns all pairwise log2 ratios between treat and control replicas.

Returns:: float[oligo index][all log2(t/c) ratios]

layeredRatios

public static double[] layeredRatios(float[][] oligoTreat,
                                     float[][] oligoCont)

Given two float[replica][values] for treat and cont, for each replica makes all pairwise ratios between treat and control.

pairedRatios

public static double[] pairedRatios(float[][] treatments,
                                    float[][] controls)

Given two float[replica][values] for treat and cont, for each replica makes matched pairwise ratios between treat and control. Must have equal number of replicas for both T and C.

pairedRelativeDifferences

public static double[] pairedRelativeDifferences(float[][] treatments,
                                                 float[][] controls)

Given two float[replica][values] for treat and cont, for each replica makes matched pairwise relative differences between treat and control. Must have equal number of replicas for both T and C.

layeredLogRatios

public static double[] layeredLogRatios(float[][] oligoTreat,
                                        float[][] oligoCont)

Given two float[replica][values] for treat and cont, for each replica makes all pairwise log2 ratios between treat and control. Zero ratios are assigned a log2 of 0.0000000001

pairedLogRatios

public static double[] pairedLogRatios(float[][] treatments,
                                       float[][] controls)

Given two float[replica][values] for treat and cont, for each replica makes matched pairwise log ratios between treat and control. Must have equal number of replicas for both T and C.

matScore

public static double matScore(float[] t,
                              float[] c)

Takes unlogged MAT normalized t-values, sorts, logs and takes a variant of a number stabilized trimmed mean ratio. Returns 1 if trimmed mean will zero the number of values.

pseudoMedian

public static double pseudoMedian(double[] d)

Returns a Hodges-Lehmann estimator, the median of all pairwise means.

squareRoots

public static float[] squareRoots(int num)

Returns the integer square root from zero to num.

pairwiseMeans

public static float[] pairwiseMeans(float[] d)

Returns all pairwise averages.

pairwiseMeansDouble

public static double[] pairwiseMeansDouble(float[] d)

Returns all pairwise averages.

partialPairwiseMeans

public static double[] partialPairwiseMeans(float[] a,
                                            float[] b)

Returns all pairwise averages between a and b but not self pairwise.

concatinate

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

Concatinates the float[]s, variable sizes OK.

concatinate

public static float[] concatinate(float[] one,
                                  float[] two)

Joins two float[]s using System.arraycopy().

subArray

public static float[][] subArray(float[][] intensities,
                                 int startIndex,
                                 int stopIndex)

Builds a sub array from part of a float[replica][intensities].

pseudoMedian

public static double[] pseudoMedian(float[][] repInt)

Calculates the pseudoMedian on each replica of intensities. If only one intensity, sets that as the pseudo median.

Parameters:: repInt - float[replica index][actual intensity values]

pseudoMedian

public static double pseudoMedian(float[] d)

Returns a Hodges-Lehmann estimator, the median of all pairwise means.

removeZeroValues

public static float[][][] removeZeroValues(float[][] t,
                                           float[][] c)

Removes zero values and their assoicated values from all arrays. Pass two float[numChips][oligoValues] representing treatment and control chips. The num oligoValues should be the same, the numChips can vary between t and c. Returns float[2][][] representing t[][] and c[][].

trimOutliers

public static float[] trimOutliers(float[] f,
                                   float cutoff,
                                   float replacement)

Sets values exceeding the cutoff to the default.

trimOutliers

public static float[][] trimOutliers(float[][] f,
                                     float cutoff,
                                     float replacement)

For each f[replica][]Sets values exceeding the cutoff to the default.

medianNormalize

public static float[] medianNormalize(float[] f,
                                      float targetMedian)

Median normalize unsorted array to a given number.

medianNormalize

public static float[][] medianNormalize(float[][] f,
                                        double targetMedian)

Median normalizes an unsorted float[][] array to a given target.

medianIgnoreZeros

public static double medianIgnoreZeros(float[] m)

Calculates the median value of a sorted float[] ignoring leading zero values!

convertToInt

public static int[] convertToInt(double[] d)

Convert to int[]

convertToDouble

public static double[] convertToDouble(int[] d)

Convert to double[]

convertToInt

public static int[] convertToInt(float[] d)

Convert to int[]

convertToFloat

public static float[] convertToFloat(int[] d)

Convert to float[]

relativeDifferences

public static double[] relativeDifferences(float[] t,
                                           float[] c)

Calculates relative differences. Uses 2 * ( (t-c)/(t+c) )

relativeDifference

public static double relativeDifference(double t,
                                        double c)

Calculates a relative difference. Uses 2 * ( (t-c)/(t+c) )

logRatios

public static double[] logRatios(double[] t,
                                 double[] c)

Calculates log base 2 ratios.

logRatios

public static double[] logRatios(float[] t,
                                 float[] c)

Calculates log base 2 ratios.

round

public static double[] round(double[] d,
                             int numDecimals)

Rounds a double[] based on number of desired decimals, ie 1 = x.x, 2 = x.xx limited to 6

round

public static double round(double d,
                           int numDecimals)

Rounds a double based on number of desired decimals, ie 1 = x.x, 2 = x.xx limited to 6

removeNaNInfinite

public static double[] removeNaNInfinite(double[] d)

Removes any NaN or Infinite

log10

public static double log10(double number)

Returns the LOG base 10 of the number.

log2

public static double log2(double number)

Returns the LOG base 2 of the number.

log2

public static float log2(float number)

Returns the LOG base 2 of the number.

minus10log10

public static double minus10log10(double pvalue)

Returns the -10 * LOG base 10 of the number.

loadInts

public static int[] loadInts(java.io.File f)

Loads a column of ints from a file into an array. Returns null if nothing found. Skips blank lines.

loadDoubles

public static double[] loadDoubles(java.io.File f)

Loads a column of double from a file into an array. Returns null if nothing found. Skips blank lines.

arrayListToInts

public static int[] arrayListToInts(java.util.ArrayList integers)

ArrayList of Integer to int[]

arrayListToDoubles

public static double[] arrayListToDoubles(java.util.ArrayList doubles)

ArrayList of Double to double[]

parseInt

public static int parseInt(java.lang.String stringInt,
                           int failNumber)

Attemps to parse an int, returns failNumber if it fails.

statFloatArray

public static void statFloatArray(float[] f,
                                  boolean printHistogram)

Calculates Min, Max, Mean, Median, Mode, and Histogram/10 for a Float[]

removeZeroValues

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

Remove zero values from float array.

getAverageInts

public static float getAverageInts(int start,
                                   int end)

Gets the average of the integers bracketed and including the start and end. (ie 3,6 returns the average of 3+4+5+6/4= 4.5)

collapseIntArray

public static int[] collapseIntArray(int[][] ints)

Assumes equal lengths of the int[]s

medianFloatArray

public static java.lang.String medianFloatArray(float[][] replicasIntensities)

Parameters:: replicasIntensities - - float[replicaNumber][associatedIntensities]
Returns:: comma delimited list of medians, one for each replica.

collapseFloatArray

public static float[] collapseFloatArray(float[][] fs)

Assumes equal lengths of the float[]s

collapsePartOfAnArray

public static float[] collapsePartOfAnArray(float[][] fs,
                                            int startIndex,
                                            int stopIndex)

Assumes equal lengths of the float[]s

collapseDoubleArray

public static double[] collapseDoubleArray(double[][] fs)

Assumes equal lengths of the double[]s

expandFloatArray

public static float[][] expandFloatArray(float[] f,
                                         int numRows,
                                         int numColumns)

Converts a float[] to float[][], must be certain about the number of rows and colmns!

averageIntArray

public static double averageIntArray(int[] f)

Averages a int[]

averageFloatArray

public static double averageFloatArray(float[] f)

Averages a float[]

findMinMaxIntValues

public static int[] findMinMaxIntValues(int[] f)

Finds min and max values of a int array.

findMinMaxFloatValues

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

Finds min and max values of an unsorted float array.

findMinMaxDoubleValues

public static double[] findMinMaxDoubleValues(double[] f)

Finds min and max values of a float array.

findMinMaxIntInt

public static int[] findMinMaxIntInt(int[][] f)

Finds min and max values of a int array.

findMinMaxFloatArrays

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

Finds min and max values of a float array.

findClosestStartIndex

public static int findClosestStartIndex(int[] positions,
                                        int key)

Finds the index of the key in the int[] but wont preceed the int[index]

findClosestEndIndex

public static int findClosestEndIndex(int[] positions,
                                      int key)

Finds the index of the key in the int[] but wont exceed the int[index]

findClosestIndexToValue

public static int findClosestIndexToValue(int[] sortedValues,
                                          int key)

Returns the index of the closest values[index] to the key. Rounds up if the value is equi distant between two indexes. Will not return an index <0 or > length-1 . Don't forget to SORT!. If identical values are present, returns the smallest index containing the key.

findClosestIndexToValue

public static int findClosestIndexToValue(float[] sortedValues,
                                          float key)

findStartStopIndexes

public static int[] findStartStopIndexes(int[] positions,
                                         int startValue,
                                         int stopValue,
                                         boolean notExact)

Finds the start and stop indexes given a sorted int[] of values and two values, one after the other, close together, otherwise just use Arrays.binarySearch. Good for huge int[] arrays. Set the notExact boolean to true if the values are potentially not exact.

standardDeviationOfDifference

public static double standardDeviationOfDifference(int[] t,
                                                   int[] c)

Calculates the standard deviation of the difference between two int[]s of the same length.

averageIntIntArray

public static double[] averageIntIntArray(int[][] ints)

Average int[][] values to double[], averages repeats [numRepeats][values]

averageFloatArrays

public static double[] averageFloatArrays(float[][] ints)

Average float[][] values to double[], averages repeats [values][numRepeats]

averageFloatArraysFlipped

public static double[] averageFloatArraysFlipped(float[][] ints)

Average float[][] values to double[], averages repeats [numChips][OligoValues]. Assumes equal number of oligos.

averageFloatArraysFlippedToFloat

public static float[] averageFloatArraysFlippedToFloat(float[][] ints)

Average float[][] values to double[], averages repeats [numChips][OligoValues]. Assumes equal number of oligos.

geoMeanFloatArraysFlipped

public static double[] geoMeanFloatArraysFlipped(float[][] ints)

Takes the geometric mean of float[][] values to double[], [numChips][OligoValues], returns the values in log base 2. Assumes equal number of oligos.

averageFloatArraysFlippedToFloats

public static float[] averageFloatArraysFlippedToFloats(float[][] ints)

Average float[][] values to float[], averages repeats [numChips][OligoValues]. Assumes equal number of oligos.

geometricMeanSkipZeros

public static double[] geometricMeanSkipZeros(float[][] ints)

Takes a geometric average of float[][] values to double[], averages repeats [numChips][OligoValues]. Assumes equal number of oligos. Skips zero values. Return in log base 10.

geometricMean

public static double[] geometricMean(float[][] ints)

Takes a geometric average of float[][] values [numChips][OligoValues]. Assumes no intensities <= 0. Returns log base 10 values.

averageIntIntArray2

public static double[] averageIntIntArray2(int[][] ints)

Average int[][] values to double[], averages values [numRepeats][values]

smoothScores

public static double[] smoothScores(double[] scores,
                                    int[] positions,
                                    int windowSize)

Uses a sliding window to smooth the scores applying a trimmed mean (drop 1 from ends) to the scores found within the window. The collection of values within the window is only an attempt to look windowSize/2 upstream and windowSize/2 downstream, not a requirement. Thus at either end of the scores possibly only 1/2 of the scores are used in making the calculation that is associated with the original score.

meanIgnoreZeros

public static double meanIgnoreZeros(float[] f)

Calculates a mean on the non zero floats, return zero if no non zero values were found.

windowAverageScores

public static double[] windowAverageScores(double[] scores,
                                           int windowSize)

Slides a window along an array, one index at a time, averaging the contents.

windowAverageScoresIgnoreZeros

public static double[] windowAverageScoresIgnoreZeros(double[] scores,
                                                      int windowSize)

Slides a window along an array, one index at a time, averaging the contents, ignores zero values.

windowAverageScoresIgnoreScore

public static float[] windowAverageScoresIgnoreScore(float[][] scores,
                                                     float scoreToIgnore,
                                                     int windowSize)

Slides a window along an array, one index at a time, averaging the contents, ignores zero values.

windowAverageScoresIgnoreScore

public static float[] windowAverageScoresIgnoreScore(float[] scores,
                                                     float scoreToIgnore,
                                                     int windowSize)

Slides a window along an array, one index at a time, averaging the contents.

windowAverageScores

public static float[] windowAverageScores(float[] scores,
                                          int windowSize)

Slides a window along an array, one index at a time, averaging the contents.

trimmedMean

public static double trimmedMean(double[] sortedFloat,
                                 double fraction)

Trims the fraction off the top and bottom, returns the mean of the remainder, rounds trimming # up. If trim number resolves to 0 will proceed returning mean.

trimmedMean

public static double trimmedMean(float[] sortedFloat,
                                 double fraction)

Trims the fraction off the top and bottom, returns the mean of the remainder, rounds trimming # up. If trim number resolves to 0 will proceed returning mean.

trimmedMean

public static double trimmedMean(double[] sortedDouble,
                                 int trimNumber)

Makes a trimmed mean, note the trim number is not a % but the number of values to drop from the beginning and end of the ordered set. Set appropriately. Be sure to submit an ordered array!

trimmedMean

public static double trimmedMean(float[] sortedFloat,
                                 int trimNumber)

Makes a trimmed mean, note the trim number is not a % but the number of values to drop from the beginning and end of the ordered set. Set appropriately. Be sure to submit an ordered array!

arrayListOfDoubleToArray

public static double[] arrayListOfDoubleToArray(java.util.ArrayList dbl)

ArrayList of Double to double[]

arrayListOfFloatToArray

public static float[] arrayListOfFloatToArray(java.util.ArrayList flt)

ArrayList of Float to float[]

aveFoldDiffCombine

public static double aveFoldDiffCombine(int[] t,
                                        int[] c)

Calculates the average fold difference between two int[]s of the same length. Takes the mean of both arrays returns the ratio.

aveFoldDiffIndividual

public static double aveFoldDiffIndividual(int[] t,
                                           int[] c)

Calculates the average fold difference between two int[]s of the same length. Calculates the ratio of each individually, then returns their average.

ratio

public static double[] ratio(double[] t,
                             double[] c)

Returns the ratio of each pair.

ratio

public static float[] ratio(float[][] t,
                            float[][] c)

Returns the ratio of each pair, averages replicas.

relativeDifferences

public static float[] relativeDifferences(float[][] t,
                                          float[][] c)

Returns the relative difference of each pair, averages replicas.

geometricMeanRatio

public static float[] geometricMeanRatio(float[][] t,
                                         float[][] c)

Returns the log2 ratio of each pair, takes a geometric mean of replicas.

logRatios

public static float[] logRatios(float[][] t,
                                float[][] c)

Returns the log2 ratio of each pair, averaging replicas.

ratio

public static double[] ratio(float[] t,
                             float[] c)

Returns the ratio of each pair.

ratio

public static double[] ratio(int[] t,
                             double[] c)

Returns the ratio of each pair.

ratio

public static double[] ratio(int[] t,
                             int[] c)

Returns the ratio of each pair.

difference

public static double[] difference(int[] t,
                                  int[] c)

Returns the difference of each pair.

difference

public static double[] difference(double[] t,
                                  double[] c)

Returns the difference of each pair.

pooledSubArray

public static float[][] pooledSubArray(float[][] treatment,
                                       float[][] control,
                                       int startIndex,
                                       int stopIndex)

Builds a pooled from part of a float[replica][intensities] for treat and control.

Parameters:: treatment - and control float[replicas][intensities]
Returns:: float[treatment(0) or control(1)][pooled intensities]

sam

public static float[] sam(float[] t,
                          float[] c,
                          double fudge)

Calculates the SAM d statistic, similar to a t-statistic with a bit of fudge added into the denominator to control for zero variance conditions. Set fudge to zero for standard unpaired T-Test.

Returns:: float[3] samScore, diff of means, variance (w/o fudge).

standardDeviation

public static double standardDeviation(int[] x)

Calculates standard deviation of an int[]

standardDeviation

public static double standardDeviation(int[] x,
                                       double mean)

Calculates standard deviation of an int[] and mean.

standardDeviation

public static double standardDeviation(float[] x)

Calculates standard deviation of an float[]

standardDeviation

public static double standardDeviation(float[] x,
                                       double mean)

Calculates standard deviation of an float[] given a mean.

standardDeviation

public static double standardDeviation(double[] x)

Calculates standard deviation of an double[]

standardDeviation

public static double standardDeviation(double[] x,
                                       double mean)

Calculates standard deviation of a double[] and mean.

standardError

public static double standardError(double[] x,
                                   double mean)

Calculates standard error of a double[] given it's mean. Spead savings

medianAbsoluteDifference

public static double medianAbsoluteDifference(float[] x,
                                              float[] y)

Calculates the median absolute difference.

calcMaxMedianAbsoluteDifference

public static double calcMaxMedianAbsoluteDifference(float[][] oligosValues)

Calculates the maximum median absolute difference between arrays of float where int[oligo index number][oligo intensity measurements]

calcMeanMedianAbsoluteDifference

public static double calcMeanMedianAbsoluteDifference(float[][] oligosValues)

Calculates the mean of the median absolute differences between arrays of float where float[oligo index number][oligo intensity measurements]

correlationCoefficient

public static double correlationCoefficient(int[] x,
                                            int[] y)

Calculates Pearson correlation coefficient, r, from two int[]s. Cannot have one int[] be uniform values, returns -2 if error.

removeZeroValues

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

Provide a float[2][0], will remove zeros from both and there matched pair. Does a pairwise zero removal, if either of the float arrays are zero both values are removed.

correlationCoefficient

public static double correlationCoefficient(float[] x,
                                            float[] y)

Calculates Pearson correlation coefficient, r, from two float[]s. Cannot have one float[] be uniform values, returns -2 if error.

correlationCoefficient

public static double correlationCoefficient(double[] x,
                                            double[] y)

Calculates Pearson correlation coefficient, r, from two double[]s

formatPercentOneFraction

public static java.lang.String formatPercentOneFraction(double num)

Converts 0.345543 to 34.6%

formatNumberOneFraction

public static java.lang.String formatNumberOneFraction(double num)

Converts a double ddd.dddddddd to sss.s

formatNumber

public static java.lang.String formatNumber(double num,
                                            int numberOfDecimalPlaces)

Converts a double ddd.dddddddd to a user determined number of decimal places right of the .

doubleArrayToString

public static java.lang.String doubleArrayToString(double[] d,
                                                   int numberOfDecimalPlaces,
                                                   java.lang.String delimiter)

Converts an array of double to a String with a defined number of decimal places and a delimiter.

doubleArrayToStringOnlyMax

public static java.lang.String doubleArrayToStringOnlyMax(double[] d,
                                                          int maxNumDec,
                                                          java.lang.String delimiter)

Converts an array of double to a String with a maximal number of defined decimal places and a delimiter. Min isn't set.

intArrayToString

public static java.lang.String intArrayToString(int[] d,
                                                java.lang.String delimiter)

Converts an array of int to a String seperated by the delimiter.

stringArrayToInts

public static int[] stringArrayToInts(java.lang.String s,
                                      java.lang.String delimiter)

Given a String of ints delimited by something, will parse or return null.

median

public static double median(double[] sorted)

Calculates Median of a sorted double[]. Copied code from WWW.

median

public static double median(int[] sorted)

Calculates Median of a sorted int[].

median

public static double median(short[] sorted)

Calculates Median of a sorted short[]. Copied code from WWW.

median

public static double median(float[] sorted)

Calculates Median of a sorted float[]. Copied code from WWW.

mean

public static float mean(float[] t)

Averages a float array.

mean

public static float[] mean(float[] one,
                           float[] two)

Averages two float[]s .

mean

public static float[][] mean(float[][] one,
                             float[][] two)

Averages two float[][]s, assumes a square.

mean

public static double mean(int[] t)

Averages a int array.

mean

public static double mean(double[] t)

Averages a double array.

meanIntegers

public static int meanIntegers(java.util.ArrayList Integers)

Averages an ArrayList of Integer objects.

meanDoubles

public static java.lang.String meanDoubles(java.util.ArrayList Doubles)

Averages an ArrayList of Double objects.

findHighestInt

public static int findHighestInt(int[] ints)

Finds and returns the biggest int in an int[].

findHighestFloat

public static float findHighestFloat(float[] ints)

Finds and returns the biggest float in an float[].

sumIntArray

public static int sumIntArray(int[] ints)

Sums an int array

modeOfHistogram

public static int[] modeOfHistogram(int[] ints)

Finds mode of a int[] histogram array, assumes one peak, returns the index position, value/frequency.

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util.gen Class Num

log10

log2

Num

relativeDifferenceToLog2Ratio

relativeDifferenceToLog2Ratio

millisecToDays

invertArray

factorial

arrayList2IntArrayArray

antiLog

antiLog

findZeros

rotateCounterClockwise

rotateClockwise

findMaxIntIndex

log2

log2Return

log2

log2Return

log2ReturnDouble

parseDoubles

parseInts

convertToZScores

convertToZScores

convertToMedianZScores

appendDouble

prependDouble

tukeyBiWeight

geometricMean

percentile

maskOutliers

countValues

countObjects

countOutliers

identifyOutliers

fetchMatrixValues

saveMatrixValues

loadMatrixValues

quartiles

zeroedFloatArray

loadFloatArray

randomSample

randomize

randomizeFirstArray

randomize

layeredRatiosSeperate

layeredRelativeDifferencesSeperate

layeredRelativeDifferences

layeredLogRatiosSeperate

layeredRatios

pairedRatios

pairedRelativeDifferences

layeredLogRatios

pairedLogRatios

matScore

pseudoMedian

squareRoots

pairwiseMeans

pairwiseMeansDouble

partialPairwiseMeans

concatinate

concatinate

subArray

pseudoMedian

pseudoMedian

removeZeroValues

trimOutliers

trimOutliers

medianNormalize

medianNormalize

medianIgnoreZeros

convertToInt

convertToDouble

convertToInt

convertToFloat

relativeDifferences

relativeDifference

logRatios

logRatios

util.gen
Class Num