ete2.coretype.arraytable.ArrayTable

Class ArrayTable

object --+ | ArrayTable

This object is thought to work with matrix datasets (like microarrays). It allows to load the matrix an access easily to row and column vectors.

Instance Methods

[hide private]

__str__(self)
str(x)

source code

__init__(self, matrix_file=None, mtype='float')
x.__init__(...) initializes x; see x.__class__.__doc__ for signature source code

get_row_vector(self, rowname)
Returns the vector associated to the given row name

source code

get_column_vector(self, colname)
Returns the vector associated to the given column name

source code

get_several_column_vectors(self, colnames)
Returns a list of vectors associated to several column names

source code

get_several_row_vectors(self, rownames)
Returns a list vectors associated to several row names

source code

remove_column(self, colname)
Removes the given column form the current dataset

source code

merge_columns(self, groups, grouping_criterion)
Returns a new ArrayTable object in which columns are merged according to a given criterion.

source code

transpose(self)
Returns a new ArrayTable in which current matrix is transposed.

source code

_link_names2matrix(self, m)
Synchronize curent column and row names to the given matrix

source code

write(self, fname, colnames=[]) source code

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

Properties

[hide private]

Inherited from object: __class__

str(self)
(Informal representation operator)

source code

str(x)

Overrides: object.__str__: (inherited documentation)

init(self, matrix_file=None, mtype=`'float'`)
(Constructor)

source code

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

Overrides: object.__init__: (inherited documentation)

merge_columns(self, groups, grouping_criterion)

source code

Returns a new ArrayTable object in which columns are
merged according to a given criterion.

'groups' argument must be a dictionary in which keys are the
new column names, and each value is the list of current
column names to be merged.

'grouping_criterion' must be 'min', 'max' or 'mean', and
defines how numeric values will be merged.

Example:
   my_groups = {'NewColumn':['column5', 'column6']}
   new_Array = Array.merge_columns(my_groups, 'max')

Class ArrayTable

__str__(self) (Informal representation operator)

__init__(self, matrix_file=None, mtype='float') (Constructor)

merge_columns(self, groups, grouping_criterion)

str(self)
(Informal representation operator)

init(self, matrix_file=None, mtype=`'float'`)
(Constructor)