A B C D E F G H I K L M O P R S T U V W _

C

calcCombinedStd(double[], double[], double, double, double, double) - Method in class EM_LLR_Utils.RegParamsEM

CalcDICERStability - Class in scripts

This script calculates DICER's stability.

CalcDICERStability() - Constructor for class scripts.CalcDICERStability

calcExp(double[], double) - Method in class EM_LLR_Utils.AbstractParamsEM

calcGi(double[], double[], double[]) - Method in class EM_LLR_Utils.RegParamsEM

calcLikelihood(double[], double[]) - Method in class EM_LLR_Utils.RegParamsEM

calcPercentile(int, MatrixData, boolean) - Static method in class math_utils.PercentileCalc

calcPercentiles(int, int, MatrixData, boolean) - Static method in class math_utils.PercentileCalc

calcPercentiles(int, int, MatrixData[], boolean) - Static method in class math_utils.PercentileCalc

calcPFMultFalse(double[], double, StatDistribution) - Method in class EM_LLR_Utils.RegParamsEM

calcPFMultTrue(double[], double, StatDistribution) - Method in class EM_LLR_Utils.RegParamsEM

calcResults() - Method in class scripts.HyperGeometricEnrichmentAnalysis

calcResults(double) - Method in class scripts.HyperGeometricEnrichmentAnalysis

calcROCscore(float[], float[]) - Static method in class math_utils.staticMathHelperMethods

calcStd(double[], double, double) - Method in class EM_LLR_Utils.AbstractParamsEM

calculateDiffStatistics(TscoresCalculator, Hashtable<String, HashSet<String>>) - Static method in class scripts.DifferentialClusteringSolutionSignificanceEstimator

calculateDiffStatistics(TscoresCalculator, LinkedList<LinkedList<String>>) - Static method in class scripts.DifferentialClusteringSolutionSignificanceEstimator

calculateDiffStatisticsForPairs(TscoresCalculator, Hashtable<String, HashSet<String>>) - Static method in class scripts.DifferentialClusteringSolutionSignificanceEstimator

This method go over all set pairs and calculate the fold change against average of random modules.

calculateDiffStatisticsForPairsForOurAlgo(TscoresCalculator, Hashtable<String, HashSet<String>>) - Static method in class scripts.DifferentialClusteringSolutionSignificanceEstimator

calculateMetaGraph() - Method in class graph_algorithms.MetaModuleFinder

claculateSimilarities() - Method in class main_scripts.TscoresCalculator

class2Correlations - Variable in class main_scripts.TscoresCalculator

classIndex - Variable in class main_scripts.DCGraphsCalculator

ComparableEdge - Class in graph_algorithms

ComparableEdge(int, int, double) - Constructor for class graph_algorithms.ComparableEdge

compareTo(ComparableEdge) - Method in class graph_algorithms.ComparableEdge

compareTo(MetaModule) - Method in class graph_algorithms.MetaModule

computePairWiseScoreMatrix(float[][], String) - Static method in class math_utils.staticMathHelperMethods

computePairWiseScoreMatrix(float[][], String, int, int) - Static method in class math_utils.staticMathHelperMethods

computeSortedScoresArray(float[][]) - Static method in class math_utils.staticMathHelperMethods

consistentCorrelationsGraph - Variable in class main_scripts.DCGraphsCalculator

consistentCorrelationsGraph - Variable in class main_scripts.DICER_main

containsGene(String) - Method in class math_utils.ExpressionMatrix

copyTwoArrays(float[][], int, int, int, int, float[], float[]) - Static method in class math_utils.staticMathHelperMethods

CorrelationsSampler - Class in scripts

This script receives as input an expression matrix file, a sample size, and two more optional parameters: from, to.

CorrelationsSampler() - Constructor for class scripts.CorrelationsSampler

createGene2IndexHash() - Method in class math_utils.ExpressionMatrix

createHeader() - Method in class math_utils.SimilarityMatrix

createNeighborsListsInGraph() - Method in class graph_algorithms.MetaModuleFinder