computeOCF

This function is used for compute OCF values of input bed files.

Parameters

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:

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)