Package Bio :: Package motifs :: Module matrix :: Class FrequencyPositionMatrix

Class FrequencyPositionMatrix

       object --+        
                |        
             dict --+    
                    |    
GenericPositionMatrix --+
                        |
                       FrequencyPositionMatrix

Instance Methods

[hide private]

normalize(self, pseudocounts=None)
create and return a position-weight matrix by normalizing the counts matrix.

source code

Inherited from GenericPositionMatrix: __getitem__, __init__, __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]

normalize(self, pseudocounts=None)

source code


create and return a position-weight matrix by normalizing the counts matrix.

If pseudocounts is None (default), no pseudocounts are added
to the counts.
If pseudocounts is a number, it is added to the counts before
calculating the position-weight matrix.
Alternatively, the pseudocounts can be a dictionary with a key
for each letter in the alphabet associated with the motif.