Get tumourevo subclonal deconvolution result paths

Get tumourevo subclonal deconvolution result paths

Usage

get_tumourevo_subclonal(
  spn,
  coverage,
  purity,
  vcf_caller,
  cna_caller,
  tool,
  sample = NULL
)

Arguments

spn

SPN identifier.

coverage

Sequencing coverage (integer).

purity

Sample purity: 0.9, 0.6, or 0.3.

vcf_caller

VCF caller: "mutect2" or "strelka".

cna_caller

CNA caller: "ascat" or "sequenza".

tool

Tool: "mobster", "pyclonevi", "ctree", or "viber".

sample

Sample name. Required for "mobster" and per-sample "ctree" results.

Value

Named list of file paths.

Examples

if (FALSE) { # \dontrun{
get_tumourevo_subclonal("SPN04", 50, 0.6, "mutect2", "sequenza",
                         "mobster", "SPN04_1.1")
get_tumourevo_subclonal("SPN04", 50, 0.6, "mutect2", "sequenza", "viber")
} # }