bsxplorer.BinomialData.from_report
- classmethod BinomialData.from_report(file: str | Path, report_type: Literal['bismark', 'cgmap', 'bedgraph', 'coverage', 'binom'], block_size_mb: int = 20, use_threads: bool = True, min_coverage: int = 2, save: str | Path | bool | None = None, dir: str | Path = PosixPath('/home/runner/work/BSXplorer/BSXplorer/docs'), **kwargs)[source]
Method to preprocess BS-seq cytosine report data by calculating methylation P-value for every cytosine (assuming distribution is binomial) that passes min_coverage threshold.
- Parameters:
file – Path to cytosine report.
report_type – Type of report. Possible types: “bismark”, “cgmap”, “bedgraph”, “coverage”.
save – Name with which preprocessed file will be saved. If not provided - input file name is being used.
min_coverage – Minimal coverage for cytosine.
block_size_mb – Block size for reading. (Block size ≠ amount of RAM used. Reader allocates approx. Block size * 20 memory for reading.)
use_threads – Do multi-threaded or single-threaded reading. If multi-threaded option is used, number of threads is defined by multiprocessing.cpu_count()
dir – Path to working dir, where file will be saved.
kwargs – Keyword agruements for reader (e.g. sequence)
- Returns:
Instance of Binom class.
- Return type: