Package transsys :: Module optim :: Class ExpressionSeriesObjective
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Class ExpressionSeriesObjective

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               object --+    
                        |    
AbstractObjectiveFunction --+
                            |
                           ExpressionSeriesObjective

Abstract base class for objective functions based on comparing observed with desired expression profiles.

Inherits unimplemented call method from AbstractObjectiveFunction.

Instance Methods [hide private]
 
__init__(self, f=None)
Construct an instance holding an empty series.
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__str__(self)
Produce a string suitable for saving the profiles.
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series_length(self)
Accessor to get the length of the expression profiles.
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readProfiles(self, f)
Read expression profiles from a file.
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Inherited from AbstractObjectiveFunction: __call__

Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, f=None)
(Constructor)

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Construct an instance holding an empty series.

Overrides: object.__init__

__str__(self)
(Informal representation operator)

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Produce a string suitable for saving the profiles.

Overrides: object.__str__

series_length(self)

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Accessor to get the length of the expression profiles.

Returns:
Length of the expression profiles, or None if no profiles contained in instance data.

readProfiles(self, f)

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Read expression profiles from a file.

The format expected by this: One line per factor, each line consists of whitespace separated words, the first word is the factor, followed by the expression levels given as floating point numbers.

All profiles must have the same length.

Parameters:
  • f - file to read from