add_metrics

Add Calling Cards metrics to the given DataFrame.

:param dataframe: a pandas DataFrame of promoter regions. :type dataframe: DataFrame :param pseudocount: pseudocount to use when calculating Calling Cards metrics. :type pseudocount: float :return: a pandas DataFrame of promoter regions with Calling Cards metrics. :rtype: DataFrame

Source code in callingcardstools/PeakCalling/yeast/call_peaks.py

def add_metrics(dataframe: pd.DataFrame, pseudocount: float = 0.2) -> pd.DataFrame:
    """
    Add Calling Cards metrics to the given DataFrame.

    :param dataframe: a pandas DataFrame of promoter regions.
    :type dataframe: DataFrame
    :param pseudocount: pseudocount to use when calculating Calling Cards
        metrics.
    :type pseudocount: float
    :return: a pandas DataFrame of promoter regions with Calling Cards
        metrics.
    :rtype: DataFrame
    """
    dataframe["callingcards_enrichment"] = enrichment_vectorized(
        dataframe["background_total_hops"],
        dataframe["experiment_total_hops"],
        dataframe["background_hops"],
        dataframe["experiment_hops"],
        pseudocount,
    )

    dataframe["poisson_pval"] = poisson_pval_vectorized(
        dataframe["background_total_hops"],
        dataframe["experiment_total_hops"],
        dataframe["background_hops"],
        dataframe["experiment_hops"],
        pseudocount,
    )

    dataframe["hypergeometric_pval"] = hypergeom_pval_vectorized(
        dataframe["background_total_hops"],
        dataframe["experiment_total_hops"],
        dataframe["background_hops"],
        dataframe["experiment_hops"],
    )

    return dataframe