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find_min_responsive

Finds the minimum number of responsive genes in a list of DataFrames.

This function takes a list of DataFrames and finds the minimum number of responsive genes in any of the DataFrames. This is used to normalize the rank response across expression data sets.

Parameters:

Name Type Description Default
data_path_list list

A list of paths to expression dataframes

 required
identifier_col_list list

A list of column names for the feature identifier in each DataFrame

 required
effect_col_list list

A list of column names for the effect in each DataFrame. If there is no effect column in the dataframe at the same index, enter None

 required
effect_thres_list list

A list of effect thresholds in each DataFrame

 required
pval_col_list list

A list of column names for the p-value in each DataFrame. If no threshold is to be applied to the dataframe at the same index, enter None

 required
pval_thres_list list

A list of p-value thresholds in each DataFrame. If no threshold is to be applied to the dataframe at the same index, enter None

 required

Returns:

Name Type Description
int int

The minimum number of responsive genes in any of the DataFrames.

Raises:

Type Description
TypeError

if data_path_list, identifier_col_list, effect_col_list, or pval_col_list is not a list. Also raised if there is an error in the min() statement after tallying number of responsive genes in each dataframe.
ValueError

if the length of data_path_list, identifier_col_list, effect_col_list, or pval_col_list is not equal.
Source code in callingcardstools/Analysis/yeast/find_min_responsive.py 
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def find_min_responsive(
    data_path_list: list,
    identifier_col_list: list,
    effect_col_list: list,
    effect_thres_list: list,
    pval_col_list: list,
    pval_thres_list: list,
) -> int:
    """
    Finds the minimum number of responsive genes in a list of DataFrames.

    This function takes a list of DataFrames and finds the minimum number of
    responsive genes in any of the DataFrames. This is used to normalize the
    rank response across expression data sets.

    Args:
        data_path_list (list): A list of paths to expression dataframes
        identifier_col_list (list): A list of column names for the feature
            identifier in each DataFrame
        effect_col_list (list): A list of column names for the effect in each
            DataFrame. If there is no effect column in the dataframe at the
            same index, enter `None`
        effect_thres_list (list): A list of effect thresholds in each DataFrame
        pval_col_list (list): A list of column names for the p-value in each
            DataFrame. If no threshold is to be applied to the dataframe at
            the same index, enter `None`
        pval_thres_list (list): A list of p-value thresholds in each DataFrame.
            If no threshold is to be applied to the dataframe at the same
            index, enter `None`

    Returns:
        int: The minimum number of responsive genes in any of the DataFrames.

    Raises:
        TypeError: if data_path_list, identifier_col_list, effect_col_list, or
            pval_col_list is not a list. Also raised if there is an error
            in the `min()` statement after tallying number of responsive
            genes in each dataframe.
        ValueError: if the length of data_path_list, identifier_col_list,
            effect_col_list, or pval_col_list is not equal.
    """
    if not isinstance(data_path_list, list):
        raise TypeError("data_path_list must be a list")
    if not isinstance(identifier_col_list, list):
        raise TypeError("identifier_col_list must be a list")
    if not isinstance(effect_col_list, list):
        raise TypeError("effect_col_list must be a list")
    if not isinstance(pval_col_list, list):
        raise TypeError("pval_col_list must be a list")

    if (
        len(data_path_list)
        != len(identifier_col_list)
        != len(data_path_list)
        != len(effect_col_list)
        != len(data_path_list)
        != len(pval_col_list)
        != len(effect_thres_list)
        != len(pval_thres_list)
    ):
        raise ValueError(
            "Length of data_path_list, identifier_col_list, "
            "effect_col_list, and pval_col_list must be equal"
        )

    for data_path in data_path_list:
        if not os.path.exists(data_path):
            raise FileNotFoundError(f"{data_path} does not exist")

    for identifier_col in identifier_col_list:
        if not isinstance(identifier_col, str):
            raise TypeError("identifier_col_list must contain only strings")

    for effect_col in effect_col_list:
        if not isinstance(effect_col, (str, type(None))):
            raise TypeError("effect_col_list must contain only strings or " "`None`")

    for pval_col in pval_col_list:
        if not isinstance(pval_col, (str, type(None))):
            raise TypeError("pval_col_list must contain only strings or " "`None`")

    for effect_thres in effect_thres_list:
        if not isinstance(effect_thres, (int, float, type(None))):
            raise TypeError("effect_thres_list must contain only numbers or " "`None`")

    for pval_thres in pval_thres_list:
        if not isinstance(pval_thres, (int, float, type(None))):
            raise TypeError("pval_thres_list must contain only numbers or " "`None`")

    df_list = [
        label_responsive_genes(
            read_in_data(
                data_path, identifier_col, effect_col, pval_col, "source", "expression"
            ),
            effect_thres,
            pval_thres,
        )
        for data_path, identifier_col, effect_col, effect_thres, pval_col, pval_thres in zip(
            data_path_list,
            identifier_col_list,
            effect_col_list,
            effect_thres_list,
            pval_col_list,
            pval_thres_list,
        )
    ]

    try:
        min_responsive = min([df["responsive"].sum() for df in df_list])
    except TypeError as exc:
        logger.error("Error in `find_min_responsive()`: %s", exc)
        raise

    return min_responsive