OCFplot

This function is used for plotting the boxplot of OCF values from computeOCF.

Parameters

OCFplot(caseocfInput=None, ctrlocfInput=None,
        outputdir=None, threads=1,
        upstream=None, labelInput=None,
        stepNum=None,  verbose=True)

• caseocfInput: list, input files of OCF values of case samples.

• ctrlocfInput: list, input files of OCF values of control samples.

• outputdir: str, output result folder, None means the same folder as input files.

• threads: int, how many thread to use.

• upstream: upstream output results, used for pipeline.

• labelInput: list, [name_of_case, name_of_control](e.g. [“HCC”, “CTR”])

• 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)