Get tumourevo signature deconvolution result paths — get_tumourevo_signatures • SCOUT

Get tumourevo signature deconvolution result paths

Usage

get_tumourevo_signatures(
  spn,
  coverage,
  purity,
  vcf_caller,
  cna_caller,
  tool,
  context = NULL
)

Arguments

spn: SPN identifier.
coverage: Sequencing coverage (integer).
purity: Sample purity (0–1).
vcf_caller: VCF caller: "mutect2" or "strelka".
cna_caller: CNA caller: "ascat" or "sequenza".
tool: Signature tool: "sigprofiler", "sparsesignatures", or "BASCULE".
context: Mutational context, e.g. "SBS96" or "ID83". Required for tool = "sigprofiler".

Value

Named list of file paths.

Examples

if (FALSE) { # \dontrun{
get_tumourevo_signatures("SPN01", 100, 0.9, "mutect2", "ascat", "BASCULE")
get_tumourevo_signatures("SPN01", 100, 0.9, "mutect2", "ascat", "sigprofiler", "SBS96")
} # }