scatter_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

scatter_cnvkit(
  sif_cnvkit = build_default_sif_list()$sif_cnvkit,
  chrs = build_default_chr_list()$canonical,
  cnr = NULL,
  cns = NULL,
  range = NULL,
  range_list = NULL,
  genes = NULL,
  margin_width = 1e+06,
  plot_by_bin = FALSE,
  trend = TRUE,
  antitarget_symbol = "@",
  segment_colour = "red",
  title = NULL,
  y_max = NULL,
  y_min = NULL,
  ...
)

Arguments

sif_cnvkit	REQUIRED Path to cnvkit sif file.oms.
range	OPTIONAL Range to show in chr:start-end format. Default none
range_list	OPTIONAL Path to BED file with range list. Default none
genes	OPTIONAL List of genes to focus on. Default none.
margin_width	OPTIONAL Default gene margin width. Default 1000000
plot_by_bin	OPTIONAL Assume all bins are the same size. Default FALSE
trend	OPTIONAL Show trendline. Default TRUE.
antitarget_symbol	OPTIONAL Show antitarget probes with this symbol. Default "@"
segment_colour	OPTIONAL Show antitarget probes with this symbol. Default "@"
title	OPTIONAL Sample title. Default NULL.
y_max	OPTIONAL Y max range. Default NULL.
y_min[OPTIONAL]	Y min range. 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.