GOPCAParams class

class gopca.GOPCAParams(params=None)

A set of GO-PCA parameters.

These parameters are for use in combination with a specific collection of gene sets. They exclude “global” GO-PCA parameters — those that are independent of the gene sets used, like the number of principal components to test.

Parameters:params (dict, optional) – Dictionary containing GO-PCA parameter values.

Notes

Parameter values can be specified upon class instantiation, or at a later time — using the set_param and set_params functions. Parameters that are left unspecified are assigned default values.

Parameters are exposed as virtual class attributes (using the __getattr__ magic).

The class also supports reading and writing of INI-style configuration files (see read_ini() and write_ini()).

check_params()

Check if the current configuration is valid.

Parameters:None
Returns:True iff no problems were found.
Return type:bool
param_defaults

Returns the default GO-PCA configuration as a dictionary.

params

Returns the GO-PCA configuration as a dictionary.

classmethod read_ini(path)

Reads GO-PCA configuration data form an INI-style text file.

Parameters:path (str) – The file path.
Returns:The GO-PCA configuration data.
Return type:gopca.GOPCAParams
reset_params()

Reset all parameters to their default values.

set_param(name, value)

Set a GO-PCA parameter.

Parameters:
  • name (str) – The parameter name.
  • value – The parameter value.
write_ini(path)

Write configuration data to an INI-style text file.

Parameters:path (str) – The file path
Returns:
Return type:None