GCCorrect

This function is used for processing GC correction on read count data in wig or csv/txt files.

Parameters

GCcorrect(readInput=None, gcwigInput=None,
          readtype=None, corrkey=None,
          outputdir=None, threads=1,
          stepNum=None, readupstream=None,
          gcupstream=None, verbose=True,)

• readInput: list, paths of input files of read counts.

• gcwigInput: list, paths of wig files of gc contents.

• readtype: int, file type of readInput, 1 for .wig, 2 for .txt/.csv.; 1 is set by default.

• corrkey: char, type of GC correction, “-” for minus, “/” for divide, “0” for process without GC correction; “/” is set by default

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

• threads: int, how many thread to use.

• stepNum: Step number for folder name.

• readupstream: upstream output results, used for pipeline.

• gcupstream: upstream output results, used for pipeline.

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

Warning

We recommend using this function in arm-level CNV detection.

Example usage:

# an example for compute arm-level CNV
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_bam = glob.glob("path_to_data/HCC/*.bam")
ctrl_bam = glob.glob("path_to_data/CTR/*.bam")

# case
switchConfigure("cancer")
case_bamCounter = bamCounter(
    bamInput=case_bam, upstream=True, verbose=verbose, stepNum="case01"
)
case_gcCounter = runCounter(
    filetype=0, upstream=True, verbose=verbose, stepNum="case02"
)
case_GCCorrect = GCCorrect(
    readupstream=case_bamCounter,
    gcupstream=case_gcCounter,
    verbose=verbose,
    stepNum="case03",
)

# ctrl
switchConfigure("normal")
ctrl_bamCounter = bamCounter(
    bamInput=ctrl_bam, upstream=True, verbose=verbose, stepNum="ctrl01"
)
ctrl_gcCounter = runCounter(
    filetype=0, upstream=True, verbose=verbose, stepNum="ctrl02"
)
ctrl_GCCorrect = GCCorrect(
    readupstream=ctrl_bamCounter,
    gcupstream=ctrl_gcCounter,
    verbose=verbose,
    stepNum="ctrl03",
)

switchConfigure("cancer")
res_computeCNV = computeCNV(
    caseupstream=case_GCCorrect,
    ctrlupstream=ctrl_GCCorrect,
    stepNum="ARMCNV",
    verbose=verbose,
)