proteometer.parse_metadata
==========================

.. py:module:: proteometer.parse_metadata


Functions
---------

.. autoapisummary::

   proteometer.parse_metadata.group_columns
   proteometer.parse_metadata.int_columns
   proteometer.parse_metadata.anova_columns
   proteometer.parse_metadata.t_test_groups


Module Contents
---------------

.. py:function:: group_columns(metadata: pandas.DataFrame, par: proteometer.params.Params) -> tuple[list[list[str]], list[str]]

   Generate the control and treatment group columns from the metadata.

   :param metadata: The metadata DataFrame with column names specified in `par`.
   :type metadata: pd.DataFrame
   :param par: The parameters object with the following attributes:
               - metadata_group_col: Column name for group.
               - metadata_sample_col: Column name for sample.
               - metadata_condition_col: Column name for condition.
               - metadata_control_condition: Control condition name.
   :type par: Params

   :returns:

             A tuple with the control and treatment
                 group information. The first element is a list of lists, where each
                 inner list contains the sample columns for each group. The second element
                 is a list of group names. Control groups are first, followed by treatment groups.
   :rtype: tuple[list[list[str]], list[str]]


.. py:function:: int_columns(metadata: pandas.DataFrame, par: proteometer.params.Params) -> list[str]

   Return a list of all the intensity columns in the metadata.

   :param metadata: The metadata DataFrame with column names specified in `par`.
   :type metadata: pd.DataFrame
   :param par: The parameters object with the following attributes:
               - metadata_sample_col: Column name for sample.
   :type par: Params

   :returns: A list of all the intensity columns in the metadata.
   :rtype: list[str]


.. py:function:: anova_columns(metadata: pandas.DataFrame, par: proteometer.params.Params) -> list[str]

   Return a list of columns for ANOVA analysis excluding pooled channel samples.

   :param metadata: The metadata DataFrame with column names specified in `par`.
   :type metadata: pd.DataFrame
   :param par: The parameters object with attributes:
               - metadata_condition_col: Column name for condition.
               - pooled_chanel_condition: Condition name for pooled channel.
               - metadata_group_col: Column name for group.
               - metadata_sample_col: Column name for sample.
   :type par: Params

   :returns: A list of sample columns excluding those in pooled channel groups.
   :rtype: list[str]


.. py:function:: t_test_groups(metadata: pandas.DataFrame, par: proteometer.params.Params) -> list[proteometer.stats.TTestGroup]

   Generate the user-defined pairwise t-test groups from the metadata.

   :param metadata: The metadata DataFrame with column names specified in `par`.
   :type metadata: pd.DataFrame
   :param par: The parameters object with the following attributes:
               - metadata_group_col: Column name for group.
               - metadata_sample_col: Column name for sample.
               - ttest_pairs: List of tuples containing the user-defined control and treatment group pairs.
   :type par: Params

   :returns: A list of TTestGroup objects with the user-defined pairwise t-test groups.
   :rtype: list[TTestGroup]