dynast.estimation.p_e
Module Contents
Functions
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Read p_e CSV as a dictionary, with group_by columns as keys. |
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Estimate background mutation rate of unlabeled RNA for a control sample |
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Estimate background mutation rate of unabeled RNA by calculating the |
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Estimate background mutation rate of unabeled RNA by calculating the |
- dynast.estimation.p_e.read_p_e(p_e_path: str, group_by: Optional[List[str]] = None) Dict[Union[str, Tuple[str, Ellipsis]], float][source]
Read p_e CSV as a dictionary, with group_by columns as keys.
- Parameters
- p_e_path
Path to CSV containing p_e values
- group_by
Columns to group by
- Returns
Dictionary with group_by columns as keys (tuple if multiple)
- dynast.estimation.p_e.estimate_p_e_control(df_counts: pandas.DataFrame, p_e_path: str, conversions: FrozenSet[FrozenSet[str]] = frozenset({frozenset({'TC'})})) str[source]
Estimate background mutation rate of unlabeled RNA for a control sample by simply calculating the average mutation rate.
- Parameters
- df_counts
Pandas dataframe containing number of each conversion and nucleotide content of each read
- p_e_path
Path to output CSV containing p_e estimates
- conversions
Conversion(s) in question
- Returns
Path to output CSV containing p_e estimates
- dynast.estimation.p_e.estimate_p_e(df_counts: pandas.DataFrame, p_e_path: str, conversions: FrozenSet[FrozenSet[str]] = frozenset({frozenset({'TC'})}), group_by: Optional[List[str]] = None) str[source]
Estimate background mutation rate of unabeled RNA by calculating the average mutation rate of all three nucleotides other than conversion[0].
- Parameters
- df_counts
Pandas dataframe containing number of each conversion and nucleotide content of each read
- p_e_path
Path to output CSV containing p_e estimates
- conversions
Conversion(s) in question, defaults to frozenset([(‘TC’,)])
- group_by
Columns to group by, defaults to None
- Returns
Path to output CSV containing p_e estimates
- dynast.estimation.p_e.estimate_p_e_nasc(df_rates: pandas.DataFrame, p_e_path: str, group_by: Optional[List[str]] = None) str[source]
Estimate background mutation rate of unabeled RNA by calculating the average CT and GA mutation rates. This function imitates the procedure implemented in the NASC-seq pipeline (DOI: 10.1038/s41467-019-11028-9).
- Parameters
- df_counts
Pandas dataframe containing number of each conversion and nucleotide content of each read
- p_e_path
Path to output CSV containing p_e estimates
- group_by
Columns to group by, defaults to None
- Returns
Path to output CSV containing p_e estimates