dynast.preprocessing.aggregation
Module Contents
Functions
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Read mutation rates CSV as a pandas dataframe. |
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Read aggregates CSV as a pandas dataframe. |
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Merge multiple aggregate dataframes into one. |
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Calculate mutation rate for each pair of bases. |
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Aggregate conversion counts for each pair of bases. |
- dynast.preprocessing.aggregation.read_rates(rates_path: str) pandas.DataFrame[source]
Read mutation rates CSV as a pandas dataframe.
- Parameters
- rates_path
Path to rates CSV
- Returns
Rates dataframe
- dynast.preprocessing.aggregation.read_aggregates(aggregates_path: str) pandas.DataFrame[source]
Read aggregates CSV as a pandas dataframe.
- Parameters
- aggregates_path
Path to aggregates CSV
- Returns
Aggregates dataframe
- dynast.preprocessing.aggregation.merge_aggregates(*dfs: pandas.DataFrame) pandas.DataFrame[source]
Merge multiple aggregate dataframes into one.
- Parameters
- dfs
Dataframes to merge
- Returns
Merged dataframe
- dynast.preprocessing.aggregation.calculate_mutation_rates(df_counts: pandas.DataFrame, rates_path: str, group_by: Optional[List[str]] = None) str[source]
Calculate mutation rate for each pair of bases.
- Parameters
- df_counts
Counts dataframe, with complemented reverse strand bases
- rates_path
Path to write rates CSV
- group_by
Column(s) to group calculations by, defaults to None, which combines all rows
- Returns
Path to rates CSV
- dynast.preprocessing.aggregation.aggregate_counts(df_counts: pandas.DataFrame, aggregates_path: str, conversions: FrozenSet[str] = frozenset({'TC'})) str[source]
Aggregate conversion counts for each pair of bases.
- Parameters
- df_counts
Counts dataframe, with complemented reverse strand bases
- aggregates_path
Path to write aggregate CSV
- conversions
Conversion(s) in question
- Returns
Path to aggregate CSV that was written