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

source code

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

Instance Methods [hide private]
new empty dictionary

__init__(self, alphabet, counts)
x.__init__(...) initializes x; see help(type(x)) 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__, __iter__, __le__, __len__, __lt__, __ne__, __new__, __repr__, __setitem__, __sizeof__, clear, copy, fromkeys, get, has_key, items, iteritems, iterkeys, itervalues, keys, pop, popitem, setdefault, update, values, viewitems, viewkeys, viewvalues

Inherited from object: __delattr__, __format__, __reduce__, __reduce_ex__, __setattr__, __subclasshook__

Class Variables [hide private]

Inherited from dict: __hash__

Properties [hide private]

Inherited from GenericPositionMatrix: anticonsensus, consensus, degenerate_consensus, gc_content

Inherited from object: __class__

Method Details [hide private]

__init__(self, alphabet, counts)
(Constructor)

source code 
x.__init__(...) initializes x; see help(type(x)) 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.