Class BEEDistanceMatrix

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Instance Methods

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__init__(self, *args, **kwargs)
Creates a BEE distance matrix

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loadFile(self, filename, sigset_dir=None)
Loads a BEE matrix from a file.

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loadMatrix(self, mat, query_filename, target_filename, sigset_dir=None, is_distance=True)
Creates a bee matrix from a numpy array.

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cohort_norm(self)

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getMatchScores(self, mask=None)

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getMatchScoresBySubject(self, mask=None)

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getNonMatchScores(self, mask=None)

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asFlatArray(self, mask=None)
query,target,score,type

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printInfo(self)

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write(self, filename)

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save(self, filename)
Writes the BEE distance matrix to file.

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saveBeeFormat(self, filename)

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histogram(self, value_range=None, bins=100, normed=True, mask=None)

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getROC(self, mask=None)

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getRank1(self, mask=None)

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stats(self)

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__str__(self)
Returns a string describing the matrix.

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__getitem__(self, index)
An accessor to quickly read matrix data

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shape(self)
Returns: the number of rows and columns.

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Method Details

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save(self, filename)

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Writes the BEE distance matrix to file. WARNING: DOES NOT HANDLE MASK MATRICES CORRECTLY!

shape(self)

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Returns:: the number of rows and columns.