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broad.pda.differentialExpression.Permutations Class Reference
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Static Public Member Functions

static MatrixWithHeaders[] permuteData (MatrixWithHeaders data, Collection< String > group1, Collection< String > group2, int numberPermutations, double[] fudgeFactors, boolean useFold, boolean paired)
 
static MatrixWithHeaders[] permuteData (MatrixWithHeaders data, Map< String, Collection< String >> groups, int numberPermutations, double[] fudgeFactors, boolean useFold, boolean paired)
 
static MatrixWithHeaders[] permuteDataByGroupSize (MatrixWithHeaders data, int groupSize, Map< String, Collection< String >> groups, int numPerm, double[] fudgeFactors, boolean useFold)
 
static MatrixWithHeaders[] permuteAndAssignFDR (MatrixWithHeaders testStats, MatrixWithHeaders data, Collection< String > group1, Collection< String > group2, int numberPermutations, double[] fudgeFactors, boolean useFold, boolean paired, double alpha)
 

Member Function Documentation

static MatrixWithHeaders [] broad.pda.differentialExpression.Permutations.permuteAndAssignFDR ( MatrixWithHeaders  testStats,
MatrixWithHeaders  data,
Collection< String >  group1,
Collection< String >  group2,
int  numberPermutations,
double[]  fudgeFactors,
boolean  useFold,
boolean  paired,
double  alpha 
)
static

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static MatrixWithHeaders [] broad.pda.differentialExpression.Permutations.permuteData ( MatrixWithHeaders  data,
Collection< String >  group1,
Collection< String >  group2,
int  numberPermutations,
double[]  fudgeFactors,
boolean  useFold,
boolean  paired 
)
static

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static MatrixWithHeaders [] broad.pda.differentialExpression.Permutations.permuteData ( MatrixWithHeaders  data,
Map< String, Collection< String >>  groups,
int  numberPermutations,
double[]  fudgeFactors,
boolean  useFold,
boolean  paired 
)
static

Here is the call graph for this function:

static MatrixWithHeaders [] broad.pda.differentialExpression.Permutations.permuteDataByGroupSize ( MatrixWithHeaders  data,
int  groupSize,
Map< String, Collection< String >>  groups,
int  numPerm,
double[]  fudgeFactors,
boolean  useFold 
)
static
The documentation for this class was generated from the following file:
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