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