broad.pda.differentialExpression.DifferentialExpression Class Reference

Collaboration diagram for broad.pda.differentialExpression.DifferentialExpression:

Public Member Functions
	DifferentialExpression (MatrixWithHeaders data, Collection< String > group1, Collection< String > group2, boolean useFold, boolean paired, int perm, double[] fudgeFactors, MatrixWithHeaders[] permutationMatrix, Map< String, FDRDistribution > fdrDists)
	DifferentialExpression (MatrixWithHeaders data, Map< String, Collection< String >> groups, boolean useFold, boolean paired, int perm, double[] fudgeFactors)
	DifferentialExpression (MatrixWithHeaders data, Collection< String > group1, Collection< String > group2, boolean useFold, boolean paired, int perm, double[] fudgeFactors, MatrixWithHeaders[] permutationMatrix)
	DifferentialExpression (MatrixWithHeaders data, Collection< String > group1, Collection< String > group2, boolean useFold, boolean paired, int perm)
	DifferentialExpression (MatrixWithHeaders data, Collection< String > group1, Collection< String > group2, boolean useFold, boolean paired)
	DifferentialExpression (MatrixWithHeaders data, Collection< String > group1, Collection< String > group2)
	DifferentialExpression (MatrixWithHeaders data, Collection< String > group1, Collection< String > group2, int perm)
Map< String, FDRDistribution >	getFDRDistribution ()
MatrixWithHeaders	getTestStatisticMatrix ()
MatrixWithHeaders	getFDRMatrix ()
MatrixWithHeaders	getAbsFDRMatrix ()
MatrixWithHeaders[]	getPermutationMatrix ()
MatrixWithHeaders	getFoldMatrix ()
MatrixWithHeaders	getFWERMatrix ()
MatrixWithHeaders	getNominalPValueMatrix ()
MatrixWithHeaders	getGenesPassingFDR (double alpha)

Constructor & Destructor Documentation

broad.pda.differentialExpression.DifferentialExpression.DifferentialExpression	(	MatrixWithHeaders	data,
		Collection< String >	group1,
		Collection< String >	group2,
		boolean	useFold,
		boolean	paired,
		int	perm,
		double[]	fudgeFactors,
		MatrixWithHeaders[]	permutationMatrix,
		Map< String, FDRDistribution >	fdrDists
	)

broad.pda.differentialExpression.DifferentialExpression.DifferentialExpression	(	MatrixWithHeaders	data,
		Map< String, Collection< String >>	groups,
		boolean	useFold,
		boolean	paired,
		int	perm,
		double[]	fudgeFactors
	)

broad.pda.differentialExpression.DifferentialExpression.DifferentialExpression	(	MatrixWithHeaders	data,
		Collection< String >	group1,
		Collection< String >	group2,
		boolean	useFold,
		boolean	paired,
		int	perm,
		double[]	fudgeFactors,
		MatrixWithHeaders[]	permutationMatrix
	)

broad.pda.differentialExpression.DifferentialExpression.DifferentialExpression	(	MatrixWithHeaders	data,
		Collection< String >	group1,
		Collection< String >	group2,
		boolean	useFold,
		boolean	paired,
		int	perm
	)

broad.pda.differentialExpression.DifferentialExpression.DifferentialExpression	(	MatrixWithHeaders	data,
		Collection< String >	group1,
		Collection< String >	group2,
		boolean	useFold,
		boolean	paired
	)

broad.pda.differentialExpression.DifferentialExpression.DifferentialExpression	(	MatrixWithHeaders	data,
		Collection< String >	group1,
		Collection< String >	group2
	)

broad.pda.differentialExpression.DifferentialExpression.DifferentialExpression	(	MatrixWithHeaders	data,
		Collection< String >	group1,
		Collection< String >	group2,
		int	perm
	)

Member Function Documentation

MatrixWithHeaders broad.pda.differentialExpression.DifferentialExpression.getAbsFDRMatrix

(

)

Map<String, FDRDistribution> broad.pda.differentialExpression.DifferentialExpression.getFDRDistribution

(

)

MatrixWithHeaders broad.pda.differentialExpression.DifferentialExpression.getFDRMatrix

(

)

MatrixWithHeaders broad.pda.differentialExpression.DifferentialExpression.getFoldMatrix

(

)

MatrixWithHeaders broad.pda.differentialExpression.DifferentialExpression.getFWERMatrix

(

)

MatrixWithHeaders broad.pda.differentialExpression.DifferentialExpression.getGenesPassingFDR

(

double

alpha

)

Here is the call graph for this function:

MatrixWithHeaders broad.pda.differentialExpression.DifferentialExpression.getNominalPValueMatrix

(

)

MatrixWithHeaders [] broad.pda.differentialExpression.DifferentialExpression.getPermutationMatrix

(

)

MatrixWithHeaders broad.pda.differentialExpression.DifferentialExpression.getTestStatisticMatrix

(

)

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The documentation for this class was generated from the following file:

• java/broad/pda/differentialExpression/DifferentialExpression.java