Get tumourevo signature deconvolution result paths

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: 0.9, 0.6, or 0.3.

vcf_caller

VCF caller: "mutect2" or "strelka".

cna_caller

CNA caller: "ascat" or "sequenza".

tool

Tool: "sigprofiler", "sparsesignatures", or "BASCULE".

context

Mutational context, e.g. "SBS96", "ID83", "DBS78". Required for tool = "sigprofiler".

Value

Named list of file paths.

Examples

if (FALSE) { # \dontrun{
get_tumourevo_signatures("SPN04", 50, 0.6, "mutect2", "sequenza", "BASCULE")
get_tumourevo_signatures("SPN04", 50, 0.6, "mutect2", "sequenza",
                          "sigprofiler", context = "SBS96")
} # }