Package Bio :: Package motifs :: Module matrix :: Class PositionWeightMatrix

Class PositionWeightMatrix

       object --+        
                |        
             dict --+    
                    |    
GenericPositionMatrix --+
                        |
                       PositionWeightMatrix

Instance Methods

[hide private]

new empty dictionary

__init__(self, alphabet, counts)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature

source code

log_odds(self, background=None)
returns the Position-Specific Scoring Matrix.

source code

Inherited from GenericPositionMatrix: __getitem__, __str__, reverse_complement

Inherited from dict: __cmp__, __contains__, __delitem__, __eq__, __ge__, __getattribute__, __gt__, __hash__, __iter__, __le__, __len__, __lt__, __ne__, __new__, __repr__, __setitem__, clear, copy, fromkeys, get, has_key, items, iteritems, iterkeys, itervalues, keys, pop, popitem, setdefault, update, values

Inherited from object: __delattr__, __reduce__, __reduce_ex__, __setattr__

Properties

[hide private]

Inherited from GenericPositionMatrix: anticonsensus, consensus, degenerate_consensus

Inherited from object: __class__

Method Details

[hide private]

init(self, alphabet, counts)
(Constructor)

source code

x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Returns: new empty dictionary
Overrides: object.__init__: (inherited documentation)

log_odds(self, background=None)

source code


returns the Position-Specific Scoring Matrix.

The Position-Specific Scoring Matrix (PSSM) contains the log-odds
scores computed from the probability matrix and the background
probabilities. If the background is None, a uniform background
distribution is assumed.

Class PositionWeightMatrix

__init__(self, alphabet, counts) (Constructor)

log_odds(self, background=None)

init(self, alphabet, counts)
(Constructor)