:py:mod:`deeprvat.utils`
========================

.. py:module:: deeprvat.utils

.. autodoc2-docstring:: deeprvat.utils
   :allowtitles:

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

Functions
~~~~~~~~~

.. list-table::
   :class: autosummary longtable
   :align: left

   * - :py:obj:`fdrcorrect_df <deeprvat.utils.fdrcorrect_df>`
     - .. autodoc2-docstring:: deeprvat.utils.fdrcorrect_df
          :summary:
   * - :py:obj:`bfcorrect_df <deeprvat.utils.bfcorrect_df>`
     - .. autodoc2-docstring:: deeprvat.utils.bfcorrect_df
          :summary:
   * - :py:obj:`pval_correction <deeprvat.utils.pval_correction>`
     - .. autodoc2-docstring:: deeprvat.utils.pval_correction
          :summary:
   * - :py:obj:`suggest_hparams <deeprvat.utils.suggest_hparams>`
     - .. autodoc2-docstring:: deeprvat.utils.suggest_hparams
          :summary:
   * - :py:obj:`compute_se <deeprvat.utils.compute_se>`
     - .. autodoc2-docstring:: deeprvat.utils.compute_se
          :summary:
   * - :py:obj:`standardize_series <deeprvat.utils.standardize_series>`
     - .. autodoc2-docstring:: deeprvat.utils.standardize_series
          :summary:
   * - :py:obj:`my_quantile_transform <deeprvat.utils.my_quantile_transform>`
     - .. autodoc2-docstring:: deeprvat.utils.my_quantile_transform
          :summary:
   * - :py:obj:`standardize_series_with_params <deeprvat.utils.standardize_series_with_params>`
     - .. autodoc2-docstring:: deeprvat.utils.standardize_series_with_params
          :summary:
   * - :py:obj:`calculate_mean_std <deeprvat.utils.calculate_mean_std>`
     - .. autodoc2-docstring:: deeprvat.utils.calculate_mean_std
          :summary:
   * - :py:obj:`safe_merge <deeprvat.utils.safe_merge>`
     - .. autodoc2-docstring:: deeprvat.utils.safe_merge
          :summary:
   * - :py:obj:`resolve_path_with_env <deeprvat.utils.resolve_path_with_env>`
     - .. autodoc2-docstring:: deeprvat.utils.resolve_path_with_env
          :summary:
   * - :py:obj:`copy_with_env <deeprvat.utils.copy_with_env>`
     - .. autodoc2-docstring:: deeprvat.utils.copy_with_env
          :summary:
   * - :py:obj:`load_or_init <deeprvat.utils.load_or_init>`
     - .. autodoc2-docstring:: deeprvat.utils.load_or_init
          :summary:
   * - :py:obj:`remove_prefix <deeprvat.utils.remove_prefix>`
     - .. autodoc2-docstring:: deeprvat.utils.remove_prefix
          :summary:
   * - :py:obj:`suggest_batch_size <deeprvat.utils.suggest_batch_size>`
     - .. autodoc2-docstring:: deeprvat.utils.suggest_batch_size
          :summary:

Data
~~~~

.. list-table::
   :class: autosummary longtable
   :align: left

   * - :py:obj:`logger <deeprvat.utils.logger>`
     - .. autodoc2-docstring:: deeprvat.utils.logger
          :summary:

API
~~~

.. py:data:: logger
   :canonical: deeprvat.utils.logger
   :value: 'getLogger(...)'

   .. autodoc2-docstring:: deeprvat.utils.logger

.. py:function:: fdrcorrect_df(group: pandas.DataFrame, alpha: float) -> pandas.DataFrame
   :canonical: deeprvat.utils.fdrcorrect_df

   .. autodoc2-docstring:: deeprvat.utils.fdrcorrect_df

.. py:function:: bfcorrect_df(group: pandas.DataFrame, alpha: float) -> pandas.DataFrame
   :canonical: deeprvat.utils.bfcorrect_df

   .. autodoc2-docstring:: deeprvat.utils.bfcorrect_df

.. py:function:: pval_correction(group: pandas.DataFrame, alpha: float, correction_type: str = 'FDR')
   :canonical: deeprvat.utils.pval_correction

   .. autodoc2-docstring:: deeprvat.utils.pval_correction

.. py:function:: suggest_hparams(config: typing.Dict, trial: optuna.trial.Trial, basename: str = '') -> typing.Dict
   :canonical: deeprvat.utils.suggest_hparams

   .. autodoc2-docstring:: deeprvat.utils.suggest_hparams

.. py:function:: compute_se(errors: numpy.ndarray) -> float
   :canonical: deeprvat.utils.compute_se

   .. autodoc2-docstring:: deeprvat.utils.compute_se

.. py:function:: standardize_series(x: pandas.Series) -> pandas.Series
   :canonical: deeprvat.utils.standardize_series

   .. autodoc2-docstring:: deeprvat.utils.standardize_series

.. py:function:: my_quantile_transform(x, seed=1)
   :canonical: deeprvat.utils.my_quantile_transform

   .. autodoc2-docstring:: deeprvat.utils.my_quantile_transform

.. py:function:: standardize_series_with_params(x: pandas.Series, std, mean) -> pandas.Series
   :canonical: deeprvat.utils.standardize_series_with_params

   .. autodoc2-docstring:: deeprvat.utils.standardize_series_with_params

.. py:function:: calculate_mean_std(x: pandas.Series, ignore_zero=True) -> pandas.Series
   :canonical: deeprvat.utils.calculate_mean_std

   .. autodoc2-docstring:: deeprvat.utils.calculate_mean_std

.. py:function:: safe_merge(left: pandas.DataFrame, right: pandas.DataFrame, validate: str = '1:1', equal_row_nums: bool = False)
   :canonical: deeprvat.utils.safe_merge

   .. autodoc2-docstring:: deeprvat.utils.safe_merge

.. py:function:: resolve_path_with_env(path: str) -> str
   :canonical: deeprvat.utils.resolve_path_with_env

   .. autodoc2-docstring:: deeprvat.utils.resolve_path_with_env

.. py:function:: copy_with_env(path: str, destination: str) -> str
   :canonical: deeprvat.utils.copy_with_env

   .. autodoc2-docstring:: deeprvat.utils.copy_with_env

.. py:function:: load_or_init(pickle_file: str, init_fn: typing.Callable) -> typing.Any
   :canonical: deeprvat.utils.load_or_init

   .. autodoc2-docstring:: deeprvat.utils.load_or_init

.. py:function:: remove_prefix(string, prefix)
   :canonical: deeprvat.utils.remove_prefix

   .. autodoc2-docstring:: deeprvat.utils.remove_prefix

.. py:function:: suggest_batch_size(tensor_shape: typing.Iterable[int], example: typing.Dict[str, typing.Any] = {'batch_size': 16384, 'tensor_shape': (20, 125, 38), 'max_mem_bytes': 22890098688}, buffer_bytes: int = 2500000000)
   :canonical: deeprvat.utils.suggest_batch_size

   .. autodoc2-docstring:: deeprvat.utils.suggest_batch_size