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)