computeOCF ========== This function is used for compute OCF values of input bed files. Parameters ~~~~~~~~~~ .. code:: python computeOCF(casebedInput=None, ctrlbedInput=None, refRegInput=None, outputdir=None, threads=1, caseupstream=None, ctrlupstream=None, labelInput=None, stepNum=None, verbose=True) - casebedInput: list, input bed files of case samples. - ctrlbedInput: list, input bed files of control samples. - refRegInput: str, reference file for OCF computing. - outputdir: str, output result folder, None means the same folder as input files. - threads: int, how many thread to use. - caseupstream: upstream output results, used for pipeline. - ctrlupstream: upstream output results, used for pipeline. - stepNum: int or str, step flag for folder name. - verbose: bool, True means print all stdout, but will be slow; False means black stdout verbose, much faster. .. warning:: We recommend using this function in OCF analysis. Example usage: .. code:: python from cfDNApipe import * import glob pipeConfigure2( threads=20, genome="hg19", refdir=r"reference_genome/hg19", outdir=r"output/pcs_armCNV", data="WGS", type="paired", JavaMem="8G", case="cancer", ctrl="normal", build=True, ) verbose = False case_bed = glob.glob("path_to_data/HCC/*.bed") ctrl_bed = glob.glob("path_to_data/CTR/*.bed") switchConfigure("cancer") res_computeOCF = computeOCF( casebedInput=case_bed, ctrlbedInput=ctrl_bed, caseupstream=True, verbose=verbose, ) res_OCFplot = OCFplot(upstream=res_computeOCF, verbose=verbose)