ichorCNA: Generate report for ULP-WGS samples

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

Generate report for ULP-WGS samples

Description

This function generates a report that helps to segment the genome, predict large-scale copy number alterations, and estimate tumor fraction in ULP-WGS samples.

Usage

ichorCNA(
  bin_ichor = build_default_tool_binary_list()$bin_ichor,
  sample_id = "",
  wig = "",
  norm_wig = "",
  bed = "",
  ploidy = "2,3",
  tumour_content = "0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9",
  homozygous_del = "False",
  subclonal_states = NULL,
  gc = "tools/ichorCNA/inst/extdata/gc_hg19_500kb.wig",
  map = "tools/ichorCNA/inst/extdata/map_hg19_500kb.wig",
  centromere = "tools/ichorCNA/inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt",
 
    normal_panel = "tools/ichorCNA/inst/extdata/HD_ULP_PoN_500kb_median_normAutosome_mapScoreFiltered_median.rds",
  output_dir = ".",
  verbose = TRUE,
  libdir = "tools/ichorCNA",
  male_tresh = 1e-04,
  chrs = "'c(1:22,\"X\")'",
  chrTrain = "'c(1:22)'"
)

Arguments

bin_ichor	Path to ichorCNA executable. Default path tools/ichorCNA/scripts/runIchorCNA.R.
sample_id	String with sample name.
wig	Path to the WIG file.
norm_wig	Path to normal WIG file.
bed	Path to BED file with target regions.
ploidy	Initial tumour ploidy. Default 2,3
tumour_content	Initial normal contamination. Default 0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9
homozygous_del	Include Homozygous deleteions. Default FALSE.
subclonal_states	Subclonal states to consider. Default NULL
gc	Path to GC-content WIG with . Default tools/ichorCNA/inst/extdata/gc_hg19_500kb.wig
map	Path to mappability score WIG with GC content. Default tools/ichorCNA/inst/extdata/map_hg19_500kb.wig
centromere	Path to file containing centromere locations. Default tools/ichorCNA/inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt
normal_panel	Path to file containing normal panel data. Default tools/ichorCNA/inst/extdata/HD_ULP_PoN_hg38_500kb_median_normAutosome_median.rds
output_dir	Path to the output directory.
verbose	Enables progress messages. Default False.
libdir	Path to dir containing ichorCNA libraries.
male_tresh	Minimum percentage of reads in chromosome Y to call male. Default 0.0001
chrs	Chromosomes to analyze. Default 'c(1:22,\"X\")'
chrsTrain	Chromosomes to estimate parameters. Default 'c(1:22)'

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