fraglenplot_comp

This function is used for compare the fragments’ lengths in case and control samples.

Note

This function do not suit for single end data.

Parameters

fraglenplot_comp(casebedInput=None, ctrlbedInput=None,
                 outputdir=None, maxLimit=500,
                 labelInput=None, threads=1,
                 stepNum=None, caseupstream=None,
                 ctrlupstream=None, verbose=True,)

• casebedInput: list, input bed files of case samples.

• ctrlbedInput: list, input bed files of control samples.

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

• maxLimit: int, maximum length to be considered.

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

• ratio1, ratio2: proportion statistics break point, default: 150, 400

• threads: int, how many thread to use.

• stepNum: int or str, step flag for folder name.

• caseupstream: upstream output results, used for pipeline.

• ctrlupstream: upstream output results, used for pipeline.

• verbose: bool, True means print all stdout, but will be slow; False means black stdout verbose, much faster.

Example usage:

from cfDNApipe import *
import glob
import pysam

pipeConfigure(
    threads=20,
    genome="hg19",
    refdir=r"path_to_genome/hg19",
    outdir=r"path_to_output/pcs_fraglen",
    data="WGS",
    type="paired",
    JavaMem="10G",
    build=True,
)

verbose = False

case_bed = glob.glob("/data/wzhang/pcs_final/HCC/*.bed")
ctrl_bed = glob.glob("/data/wzhang/pcs_final/Healthy/*.bed")

res_fraglenplot_comp = fraglenplot_comp(
    casebedInput=case_bed, ctrlbedInput=ctrl_bed, caseupstream=True, verbose=verbose)