computeDMR

This function is used for compute DMR between case and aontrol samples.

Parameters

computeDMR(casetxtInput=None, ctrltxtInput=None,
           outputdir=None, threads=1, diff=0.2, adjmethod=None,
           caseupstream=None, ctrlupstream=None, stepNum=None)

  • casetxtInput: list, input methylation level files of case samples.

  • ctrlbedInput: list, input methylation level files of control samples.

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

  • threads: int, how many thread to use.

  • diff: minimal mean difference between two group, default:0.2.

  • adjmethod: str, method of p_value correction, must be “bonferroni”, “fdr_bh”(default), “fdr_by” or “holm”

  • caseupstream: upstream output results, used for pipeline.

  • ctrlupstream: upstream output results, used for pipeline.

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

Example usage:

# this function is used for bismark output

from cfDNApipe import *

pipeConfigure2(
    threads=60,
    genome="hg19",
    refdir="path_to_reference/hg19_bismark",
    outdir="path_to_output/WGBS_single",
    data="WGBS",
    type="single",
    case="HCC",
    ctrl="Healthy",
    JavaMem="10G",
    build=True,
)

# case_calMethy and ctrl_calMethy are from function calculate_methyl
switchConfigure("HCC")
computeDMR(caseupstream=case_calMethy, ctrlupstream=ctrl_calMethy, adjmethod="fdr_bh")