Fragmentomics¶
The Following example shows how to perform OCF and fragmentation profile analysis. For up- and down-stream relationship, please see “Up Down Stream Flowchart” part.
OCF 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)
fragmentation profile 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_bedgz = glob.glob("path_to_data/HCC/*.bed.gz")
ctrl_bedgz = glob.glob("path_to_data/CTR/*.bed.gz")
# case
switchConfigure("cancer")
case_fragCounter = fpCounter(
bedgzInput=case_bedgz, upstream=True, verbose=verbose, stepNum="case01", processtype=1
)
case_gcCounter = runCounter(
filetype=0, binlen=5000000, upstream=True, verbose=verbose, stepNum="case02"
)
case_GCCorrect = GCCorrect(
readupstream=case_fragCounter,
gcupstream=case_gcCounter,
readtype=2,
corrkey="-",
verbose=verbose,
stepNum="case03",
)
# ctrl
switchConfigure("normal")
ctrl_fragCounter = fpCounter(
bedgzInput=ctrl_bedgz, upstream=True, verbose=verbose, stepNum="ctrl01", processtype=1
)
ctrl_gcCounter = runCounter(
filetype=0, binlen=5000000, upstream=True, verbose=verbose, stepNum="ctrl02"
)
ctrl_GCCorrect = GCCorrect(
readupstream=ctrl_fragCounter,
gcupstream=ctrl_gcCounter,
readtype=2,
corrkey="-",
verbose=verbose,
stepNum="ctrl03",
)
switchConfigure("cancer")
res_fragprofplot = fragprofplot(
caseupstream=case_GCCorrect,
ctrlupstream=ctrl_GCCorrect,
stepNum="FP",
)