Methylation Analysis

The Following example shows how to perform deconvolution analysis. For up- and down-stream relationship, please see “Up Down Stream Flowchart” part.

deconvolution Example usage

import glob
from cfDNApipe import *

pipeConfigure2(
   threads=100,
   genome="hg19",
   refdir=r"path_to_reference/hg19_bismark",
   outdir=r"path_to_output/WGBS",
   data="WGBS",
   type="single",
   case="HCC",
   ctrl="Healthy",
   JavaMem="10G",
   build=True,
)

hcc = glob.glob("/WGBS/HCC/intermediate_result/step_06_compress_methyl/*.gz")
ctr = glob.glob("/WGBS/Healthy/intermediate_result/step_06_compress_methyl/*.gz")

verbose = False

switchConfigure("HCC")
hcc1 = calculate_methyl(tbxInput=hcc, bedInput="plasmaMarkers_hg19.bed", upstream=True, verbose=verbose)
hcc2 = deconvolution(upstream=hcc1)

switchConfigure("Healthy")
ctr1 = calculate_methyl(tbxInput=ctr, bedInput="plasmaMarkers_hg19.bed", upstream=True, verbose=verbose)
ctr2 = deconvolution(upstream=ctr1)