diagram_cnvkit: Wrapper around reference scatter from CNVkit

In TearsWillFall/ULPwgs: An implementation of a wrapper for estimating tumor fraction in ultra-low-pass whole genome sequencing (ULP-WGS) for cell-free DNA in GNU/Unix based systems

Wrapper around reference scatter from CNVkit

Description

This function wraps around target function for CNVkit This function generates an target BED file from an input target file. Additional parameters can be used to exclude regions and modify the average bin size

Usage

diagram_cnvkit(
  chrs = build_default_chr_list()$canonical,
  sif_cnvkit = build_default_sif_list()$sif_cnvkit,
  cnr = NULL,
  cns = NULL,
  cn_thr = 0.5,
  min_probes = 3,
  male_reference = FALSE,
  gender = "male",
  shift = TRUE,
  title = NULL,
  ...
)

Arguments

sif_cnvkit	REQUIRED Path to cnvkit sif file.oms.
cnr	REQUIRED Path to CNR as produced by fix_cnvkit command.
cns	OPTIONAL Path to CNS as produced by segment_cnvkit command.
cn_thr	OPTIONAL Copy number threshold. Default 0.5
min_probes	OPTIONAL Minimum number of probes to show a gene. Default 3
male_reference	OPTIONAL Assume inputs were normalized to a male reference. Default FALSE
gender	OPTIONAL Assume sample gender. Default male
shift	OPTIONAL Adjust the X and Y chromosomes according to sample sex. Default TRUE
title	OPTIONAL Sample ID. Default NULL.
output_name	OPTIONAL Name for the output. If not given the name of the first tumour sample of the samples will be used.
output_dir	OPTIONAL Path to the output directory.
threads	OPTIONAL Number of threads to split the work. Default 4
ram	OPTIONAL RAM memory to asing to each thread. Default 4
verbose	OPTIONAL Enables progress messages. Default False.
mode	REQUIRED Where to parallelize. Default local. Options "local","batch"
executor_id	Task EXECUTOR ID. Default "recalCovariates"
task_name	Task name. Default "recalCovariates"
time	OPTIONAL If batch mode. Max run time per job. Default "48:0:0"
update_time	OPTIONAL If batch mode. Job update time in seconds. Default 60.
wait	OPTIONAL If batch mode wait for batch to finish. Default FALSE
hold	OPTIONAL HOld job until job is finished. Job ID.

Details

For more information read: https://cnvkit.readthedocs.io/en/stable/pipeline.html

TearsWillFall/ULPwgs documentation built on April 18, 2024, 3:45 p.m.