deconvolution

This function is used for methylation signal deconvolution.

Parameters

deconvolution(mixInput=None, refInput=None,
              outputdir=None, threads=1, stepNum=None,
              upstream=None, marker_path='', scale=0.1,
              delcol_factor=10, iter_num=10,
              confidence=0.75, w_thresh=10,
              unknown=False, is_markers=False,
              is_methylation=True)

• mixInput: Input samples need to be deconvoluted.

• refInput: reference files. Default from https://www.pnas.org/content/112/40/E5503.

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

• threads: int, how many thread to use. In this function, this number is set to 1.

• upstream: upstream output results, used for pipeline, must from calculate_methyl.

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

• marker_path: str, path to markers, if users select to specify certain markers

• scale: float, control the convergence of SVR

• delcol_factor: int, control the extent of removing collinearity

• iter_num: int, iterative numbers of outliers detection

• confidence: float, ratio of remained markers in each outlier detection loop

• w_thresh: int, threshold to cut the weights designer

• unknown: bool, if there is unknown content

• is_markers: bool, if users choose to specify their own markers

Warning

We recommend using this function with bismark related functions.

Example usage:

from cfDNApipe import *

pipeConfigure(
    threads=60,
    genome="hg19",
    refdir=r"path_to_reference/hg19_bismark",
    outdir=r"path_to_output/WGBS",
    data="WGBS",
    type="paired",
    build=True,
    JavaMem="10g",
)

fq1 = ["test1_1.fq", "test2_1.fq"]
fq2 = ["test1_2.fq", "test2_2.fq"]

res_bismark = bismark(seqInput1=fq1, seqInput2=fq2,
                      ref="path_to_bismark_genome",
                      upstream=True, threads=30, paired=True)

res_deduplicate = bismark_deduplicate(
    upstream=res_bismark, other_params=dudupOP, verbose=verbose
)

res_methyextract = bismark_methylation_extractor(
    upstream=res_deduplicate, other_params=extractMethyOP, verbose=verbose
)

res_compressMethy = compress_methyl(upstream=res_methyextract, verbose=verbose)

res_calMethy = calculate_methyl(
    upstream=res_compressMethy, bedInput=methyRegion, verbose=verbose
)
res_deconvolution = deconvolution(upstream=res_calMethy)