facets_cna_consensus: Consensus CNA estimation and plotting with Facets input All...

In brucemoran/somenone: R functions required by the somenone NextFlow nf-core pipeline

Consensus CNA estimation and plotting with Facets input All files being matched to be contained in work_dir

Description

Consensus CNA estimation and plotting with Facets input All files being matched to be contained in work_dir

Usage

facets_cna_consensus(
  cncf_match,
  pp_match,
  dict_file,
  tag,
  cgc_bed = NULL,
  work_dir = NULL
)

Arguments

cncf_match	character matched for a cncf format output of facets
pp_match	character path to a ploidy/purity format output of facets
dict_file	character string name of dictionary file for the fasta used to align data
tag	a string used to tag output
cgc_bed	bedfile from the Cancer Gene Census from COSMIC
work_dir	character path of where files should be found, written (default: ./)

Value

none, saves plots and data in current dir

brucemoran/somenone documentation built on Nov. 1, 2022, 3:56 p.m.